Copyright: Copyright (C) 1998 Klaus Brandenburg -   Mon Dec 21 15:57:15 1998


 Diamond Help Index

The Diamond Help Library gives you unified access to the Diamond online help. The library consists of the following parts:

(1) An introduction to Diamond

(2) An overview for experienced users of Diamond 1.x what is new in version 2.0.

(3) An online user manual.

(4) A tutorial which will make you familiar with the wide variety of functions in Diamond.

(5) A list of hints and tips.

Additionally, the Help Library contains context-sensitive help for commands, toolbar buttons, and dialog boxes. This help is available with the F1 key.

For the latest versions of Diamond help files, visit the Diamond support page on the Web (http://www.crystalimpact.com/diamond/support.htm). The Diamond page will also offer answers to many commonly asked questions and new information about Diamond that may not appear in the documentation.

If a dialog box is open, specific help about the controls in the dialog box is available. In most cases, you may go further to related topics of the online user manual, which is part of the Diamond Help Library. Furthermore, context-sensitive help is available for a menu item, if that is focussed with the mouse. For example, if you open the File menu and move the selection to the Print command, and then press F1, you will get help for the Print command.

If neither menu nor dialog box have the input focus, this general overview will be displayed.

The [image] button in the standard toolbar offers a more versatile method of getting context-sensitive help. After this button has been pushed, the mouse cursor changes to a symbol consisting of standard arrow and question mark. In this mode, you will get context-sensitive help, if you click on a menu item or a symbol in a toolbar or on special parts of the Diamond application window, such as the status bar, system menu etc.

For an introducing overview about online help in Diamond and the Diamond Help Library, see the article "About Diamond Online Help".


File menu commands

The File menu offers the following commands:

New	Creates a new document.
Open	Opens an existing document.
Close	Closes an opened document.
Save	Saves an opened document using the same file name.
Save As	Saves an opened document to a specified file name.
Print	Prints a document.
Print Preview	Displays the document on the screen as it would appear printed.
Print Setup	Selects a printer and printer connection.
Send...	Sends the active document through electronic mail.
Exit	Exits <<YourApp>>.


Edit menu commands

The Edit menu offers the following commands:

Undo	Reverse previous editing operation.
Cut	Deletes data from the document and moves it to the clipboard.
Copy	Copies data from the document to the clipboard.
Paste	Pastes data from the clipboard into the document.
Paste Link	Pastes from the clipboard a link to data in another application.
Insert New Object	Inserts and embeds an object, such as a chart or an equation in a document.
Links	List and edit links to embedded documents.


View menu commands

The View menu offers the following commands:

Toolbar	Shows or hides the toolbar.
Status Bar	Shows or hides the status bar.


Window menu commands

The Window menu offers the following commands, which enable you to arrange multiple views of multiple documents in the application window:

New Window	Creates a new window that views the same document.
Cascade	Arranges windows in an overlapped fashion.
Tile	Arranges windows in non-overlapped tiles.
Arrange Icons	Arranges icons of closed windows.
Split	Split the active window into panes.
Window 1, 2, ...	Goes to specified window.


Help menu commands

The Help menu offers the following commands, which provide you assistance with this application:

Help Topics	Offers you an index to topics on which you can get help.
About	Displays the version number of this application.


New command (File menu)

Use this command to create a new structure "document" in Diamond. A new structure has the following default values: Lattice constants a = b = c = 1 Å, alpha = beta = gamma = 90°; space group P1; no atomic parameters.

If you want to open an existing structure file, use the Open command from the File menu, instead.

Shortcuts

Toolbar:

Keys:	CTRL+N

See also:

Opening and Closing of Structure Windows

New Structure Window


File New dialog box

<< Delete this help topic if your application supports only one document type. >>

Specify the type of document you wish to create:

<< List your application's document types here >>


Open command (File menu)

Use this command to open an existing structure document in a new window.

You can create new documents with the New command from the File menu, instead.

Shortcuts

Toolbar:

Keys:	CTRL+O

See also:

Opening and Closing of Structure Windows

Files: Overview


File Open dialog box

The following options allow you to specify which file to open:

File Name

Type or select the filename you want to open.  This box lists files with the extension you select in the List Files of Type box.

List Files of Type

Select the type of file you want to open:

<< List your application's file types here. >>

Drives

Select the drive in which Diamond stores the file that you want to open.

Directories

Select the directory in which Diamond stores the file that you want to open.

Network...

Choose this button to connect to a network location, assigning it a new drive letter.


Close command (File menu)

Use this command to close the active structure window. Diamond suggests that you save changes to your structure document before you close it. If you close a document without saving, you lose all changes made since the last time you saved it. Before closing an untitled document, Diamond displays the Save As dialog box and suggests that you name and save the structure document.

See also:

Opening and Closing of Structure Windows


Save command (File menu)

Use this command to save the active document to its current name and directory.  When you save a document for the first time, Diamond displays the Save As dialog so you can name your document.  If you want to change the name and directory of an existing document before you save it, choose the Save as command from the File menu.

Shortcuts

Toolbar:

Keys:	CTRL+S

See also:

Files: Overview


Save As command (File menu)

Use this command to save and name the active document. Diamond displays the Save as dialog so you can name your structure document.

To save a document with its existing name and directory, use the Save command from the File menu.

See also:

Files: Overview


Send command (File menu)

Use this command to send the active document through electronic mail.  This command presents a mail window with the active document attached to it.  You may then fill out the To: field, Subject: field, etc., and add text to the body of the message if you wish.  When you are finished you may click the "Send" button to send the message.


File Save As dialog box

The following options allow you to specify the name and location of the file you're about to save:

File Name

Type a new filename to save a document with a different name.  A filename can contain up to eight characters and an extension of up to three characters.  Diamond adds the extension you specify in the Save File As Type box.

Drives

Select the drive in which you want to store the document.

Directories

Select the directory in which you want to store the document.

Network...

Choose this button to connect to a network location, assigning it a new drive letter.

<< Add other File Save As dialog box options depending on which ones your application chooses via the OFN_ flags of the OPENFILENAME structure used by the CFileDialog. >>


1, 2, 3, 4, 5, 6, 7, 8 command (File menu)

Use the numbers and filenames listed at the bottom of the File menu to open the last eight documents you closed.  Choose the number that corresponds with the document you want to open.

See also:

Files: Overview


Exit command (File menu)

Use this command to end your Diamond session. You can also use the Close command on the application Control menu. Diamond prompts you to save documents with unsaved changes.

Shortcuts

Mouse:	Double-click the application's Control menu button.

Keys:	ALT+F4


Cut command (Edit menu)

Use this command to remove the currently selected data from the document and put it on the clipboard.  This command is unavailable if there is no data currently selected.

Cutting data to the clipboard replaces the contents previously stored there.

Shortcuts

Toolbar:

Keys:	CTRL+X

Remark

Cutting of data is not available in Diamond in the current version.


Copy command (Edit menu)

Copies the contents of the structure picture onto the clipboard, if the structure pane is active. Otherwise the selected part of the secondary pane will be copied as text onto the clipboard.

Copying data to the clipboard replaces the contents previously stored there.

Shortcuts

Toolbar:

Keys:	CTRL+C

See also:

Copying the Contents of the Structure Picture

Copying and Printing Data from the Data Sheet


Paste command (Edit menu)

Use this command to insert a copy of the clipboard contents at the insertion point.  This command is unavailable if the clipboard is empty.

Shortcuts

Toolbar:

Keys:	CTRL+V

Remark

This command is not available in the current version of Diamond.


Toolbar command (View menu)

Use this command to display and hide the Toolbar, which includes buttons for some of the most common commands in Diamond, such as File Open.  A check mark appears next to the menu item when the Toolbar is displayed.

See Toolbar for help on using the toolbar.


Toolbar

The toolbar is displayed across the top of the application window, below the menu bar.  The toolbar provides quick mouse access to many tools used in Diamond,

To hide or display the Toolbar, choose Toolbar from the View menu (ALT, V, T).

<< Add or remove toolbar buttons from the list below according to which ones your application offers. >>

Click	To

Open a new document.

Open an existing document.  Diamond displays the Open dialog box, in which you can locate and open the desired file.

Save the active document or template with its current name.  If you have not named the document, Diamond displays the Save As dialog box.

Print the active document.

Remove selected data from the document and stores it on the clipboard.

Copy the selection to the clipboard.

Insert the contents of the clipboard at the insertion point.

Reverse the last editing.  Note:  You cannot undo some actions.

Go to the first record in the current selection.

Go to the previous record in the current selection.

Go to the next record in the current selection.

Go to the last record in the current selection.


Status Bar command (View menu)

Use this command to display and hide the Status Bar, which describes the action to be executed by the selected menu item or depressed toolbar button, and keyboard latch state. A check mark appears next to the menu item when the Status Bar is displayed.

See Status Bar for help on using the status bar.


Status Bar

The status bar is a control bar with a row of text output panes, or “indicators”, at the bottom of the Diamond application window. The main part (beginning at the left) displays either result messages or brief help for the menu or toolbar command where the mouse cursor is just pointing to.

During lengthy processes, such as filling of larger cell ranges or displaying a rendered picture with some hundreds of atoms, the progress of the operation will be displayed, like in the following example:

At the right end of the status bar, four panes, called "indicators", show the actual number of:

•	atoms in the parameter list,

•	created atoms,

•	bonds between created atoms,

•	and coordination polyhedra.

Whenever a progress bar is displayed in the status bar, the corresponding operation (e.g. filling a cell range or creating an enhanced picture) can be cancelled by pressing the Ctrl+Break key combination.


New command (Window menu)

Use this command to open a new window with the same contents as the active window.  You can open multiple document windows to display different parts or views of a document at the same time.  If you change the contents in one window, all other windows containing the same document reflect those changes.  When you open a new window, it becomes the active window and is displayed on top of all other open windows.


Cascade command (Window menu)

Use this command to arrange multiple opened windows in an overlapped fashion.


Tile command (Window menu)

Use this command to arrange multiple opened windows in a non-overlapped fashion.


Tile Horizontal command (Window menu)

Use this command to vertically arrange multiple opened windows in a non-overlapped fashion.


Tile Vertical command (Window menu)

Use this command to arrange multiple opened windows side by side.


Arrange Icons Command (Window menu)

Use this command to arrange the icons for minimized windows at the bottom of the main window.  If there is an open document window at the bottom of the main window, then some or all of the icons may not be visible because they will be underneath this document window.


Split Command (Window menu)

Use this command to split the active window into panes.  You may then use the mouse or the keyboard arrows to move the splitter bars.  When you are finished, press the mouse button or enter to leave the splitter bars in their new location.  Pressing escape keeps the splitter bars in their original location.  << In a single document interface application, this command will appear on the View menu. >>


1, 2, ... command (Window menu)

Diamond displays a list of currently open document windows at the bottom of the Window menu.  A check mark appears in front of the document name of the active window.  Choose a document from this list to make its window active.


Index command (Help menu)

Use this command to display the opening screen of Help.  From the opening screen, you can jump to step-by-step instructions for using Diamond and various types of reference information.

Once you open Help, you can click the Contents button whenever you want to return to the opening screen.


Using Help command (Help menu)

Use this command for instructions about using Help.


About command (Help menu)

Use this command to display the copyright notice and version number of your copy of Diamond.


Help Using Help Command
Context Help command

Use the Context Help command to obtain help on some portion of Diamond.  When you choose the Toolbar's Context Help button, the mouse pointer will change to an arrow and question mark.  Then click somewhere in the Diamond window, such as another Toolbar button.  The Help topic will be shown for the item you clicked.

Shortcut

Keys:	SHIFT+F1


Title Bar

<< Show your application's title bar here. >>

The title bar is located along the top of a window.  It contains the name of the application and document.

To move the window, drag the title bar.  Note: You can also move dialog boxes by dragging their title bars.

A title bar may contain the following elements:

Application Control-menu button

Document Control-menu button

Maximize button

Minimize button

Name of the application

Name of the document

Restore button


Scroll bars

Displayed at the right and bottom edges of the document window.  The scroll boxes inside the scroll bars indicate your vertical and horizontal location in the document.  You can use the mouse to scroll to other parts of the document.

<< Describe the actions of the various parts of the scrollbar, according to how they behave in your application. >>


Size command (System menu)

Use this command to display a four-headed arrow so you can size the active window with the arrow keys.

After the pointer changes to the four-headed arrow:

1.	Press one of the DIRECTION keys (left, right, up, or down arrow key) to move the pointer to the border you want to move.

2.	Press a DIRECTION key to move the border.

3.	Press ENTER when the window is the size you want.

Note:  This command is unavailable if you maximize the window.

Shortcut

Mouse:	Drag the size bars at the corners or edges of the window.


Move command (Control menu)

Use this command to display a four-headed arrow so you can move the active window or dialog box with the arrow keys.

Note:  This command is unavailable if you maximize the window.

Shortcut

Keys:	CTRL+F7


System Minimize Command
Minimize command (application Control menu)

Use this command to reduce the Diamond window to an icon.

Shortcut

Mouse:	Click the minimize icon [image] on the title bar.

Keys:	ALT+F9


Maximize command (System menu)

Use this command to enlarge the active window to fill the available space.

Shortcut

Mouse:	Click the maximize icon [image] on the title bar; or double-click the title bar.

Keys:	CTRL+F10 enlarges a document window.


Next Window command (document Control menu)

Use this command to switch to the next open document window.  Diamond determines which window is next according to the order in which you opened the windows.

Shortcut

Keys:	CTRL+F6


Previous Window command (document Control menu)

Use this command to switch to the previous open document window.  Diamond determines which window is previous according to the order in which you opened the windows.

Shortcut

Keys:	SHIFT+CTRL+F6


Close command (Control menus)

Use this command to close the active window or dialog box.

Double-clicking a Control-menu box is the same as choosing the Close command.

Note:  If you have multiple windows open for a single document, the Close command on the document Control menu closes only one window at a time.  You can close all windows at once with the Close command on the File menu.

Shortcuts

Keys: 	CTRL+F4 closes a document window

ALT+F4 closes the <<YourType>> window or dialog box


Restore command (Control menu)

Use this command to return the active window to its size and position before you chose the Maximize or Minimize command.


Switch to command (application Control menu)

Use this command to display a list of all open applications.  Use this "Task List" to switch to or close an application on the list.

Shortcut

Keys:	CTRL+ESC

Dialog Box Options

When you choose the Switch To command, you will be presented with a dialog box with the following options:

Task List

Select the application you want to switch to or close.

Switch To

Makes the selected application active.

End Task

Closes the selected application.

Cancel

Closes the Task List box.

Cascade

Arranges open applications so they overlap and you can see each title bar.  This option does not affect applications reduced to icons.

Tile

Arranges open applications into windows that do not overlap.  This option does not affect applications reduced to icons.

Arrange Icons

Arranges the icons of all minimized applications across the bottom of the screen.


View Ruler Command
Ruler command (View menu)

<< Write application-specific help here. >>


Choose Font Dialog
Choose Font dialog box

<< Write application-specific help here. >>


Choose Color Dialog
Choose Color dialog box

<< Write application-specific help here. >>


Edit Find Command
Find command (Edit menu)

<< Write application-specific help here. >>


Find Dialog
Find dialog box

<< Write application-specific help here. >>


Edit Replace Command
Replace command (Edit menu)

<< Write application-specific help here. >>


Replace Dialog
Replace dialog box

<< Write application-specific help here. >>


Edit Repeat Command
Repeat command (Edit menu)

Use this command to repeat the last editing command carried out.  The Repeat menu item changes to Can't Repeat if you cannot repeat your last action.

Shortcut

Key:	F4


Edit Clear Command
Clear command (Edit menu)

<< Write application-specific help here. >>


Edit Clear All
Clear All command (Edit menu)

<< Write application-specific help here. >>


Next Pane Command
Next Pane

<< Write application-specific help here. >>


Prev Pane Command
Prev Pane

<< Write application-specific help here. >>


Context-sensitive help

In Diamond, context-sensitive help is available by pressing the F1 key:

If a dialog box is open, specific help about the controls in the dialog box is available. In most cases, you may go further to related topics of the online user manual, which is part of the Diamond Help Library. Furthermore, context-sensitive help is available for a menu item, if that is focussed with the mouse. For example, if you open the File menu and move the selection to the Print command, and then press F1, you will get help for the Print command.

If neither menu nor dialog box have the input focus, this general overview will be displayed.

The [image] button in the standard toolbar offers a more versatile method of getting context-sensitive help. After this button has been pushed, the mouse cursor changes to a symbol consisting of standard arrow and question mark. In this mode, you will get context-sensitive help, if you click on a menu item or a symbol in a toolbar or on special parts of the Diamond application window, such as the status bar, system menu etc.

For an introducing overview about online help in Diamond and the Diamond Help Library, see the article "About Diamond Online Help".


No Help Available

No help is available for this area of the window.


No Help Available

No help is available for this message box.

<< If you wish to author help specific to each message box prompt, then remove the AFX_HIDP_xxx values from the [ALIAS] section of your .HPJ file, and author a topic for each AFX_HIDP_xxx value.  For example, AFX_HIDP_INVALID_FILENAME is the help topic for the Invalid Filename message box. >>


Print dialog box

The following options allow you to specify how the document should be printed:

Printer

This is the active printer and printer connection.  Choose the Setup option to change the printer and printer connection.

Setup

Displays a Print Setup dialog box, so  you can select a printer and printer connection.

Print Range

Specify the pages you want to print:

All	Prints the entire document.
Selection	Prints the currently selected text.
Pages	Prints the range of pages you specify in the From and To boxes.
Copies

Specify the number of copies you want to print for the above page range.

Collate Copies

Prints copies in page number order, instead of separated multiple copies of each page.

Print Quality

Select the quality of the printing.  Generally, lower quality printing takes less time to produce.


Print Progress Dialog

The Printing dialog box is shown during the time that Diamond is sending output to the printer.  The page number indicates the progress of the printing.

To abort printing, choose Cancel.


File Print Preview command
Print Preview command (File menu)

Use this command to display the active document as it would appear when printed.  When you choose this command, the main window will be replaced with a print preview window in which one or two pages will be displayed in their printed format.  The print preview toolbar offers you options to view either one or two pages at a time; move back and forth through the document; zoom in and out of pages; and initiate a print job.


Print Preview toolbar

The print preview toolbar offers you the following options:

Print

Bring up the print dialog box, to start a print job.

Next Page

Preview the next printed page.

Prev Page

Preview the previous printed page.

One Page / Two Page

Preview one or two printed pages at a time.

Zoom In

Take a closer look at the printed page.

Zoom Out

Take a larger look at the printed page.

Close

Return from print preview to the editing window.


File Print Setup command
Print Setup command (File menu)

Use this command to select a printer and a printer connection.  This command presents a Print Setup dialog box, where you specify the printer and its connection.


Print Setup dialog box

The following options allow you to select the destination printer and its connection.

Printer

Select the printer you want to use.  Choose the Default Printer; or choose the Specific Printer option and select one of the current installed printers shown in the box.  You install printers and configure ports using the Windows Control Panel.

Orientation

Choose Portrait or Landscape.

Paper Size

Select the size of paper that the document is to be printed on.

Paper Source

Some printers offer multiple trays for different paper sources.  Specify the tray here.

Options

Displays a dialog box where you can make additional choices about printing, specific to the type of printer you have selected.

Network...

Choose this button to connect to a network location, assigning it a new drive letter.


File Page Setup Command
Page Setup command (File menu)

<< Write application-specific help here. >>


Paste Link command
Paste Link command (Edit menu)

<< Write a topic here that talks about the kinds of objects you expect users to embed in your application's documents. >>


Edit Links command
Links command (Edit menu)

Use this command to display a  Links dialog box which lets you edit links between your document and other documents.

This command is unavailable if you have no links in your document.


Links dialog box

<< Write a topic here that discusses the Links dialog box. >>


Object verb
Object verb (Edit menu)

<< Write a topic here that discusses Object verb. >>

Shortcut

Mouse:	Double-click the object with the left mouse button.


Insert Object command
Insert New Object command (Edit menu)

Inserts and embeds an object, such as a chart or an equation in a document. The application in which the object was created becomes active on the screen.

Select the object you want to insert into your document using the Insert New Object dialog box.


Insert New Object dialog box

<< Write a topic here that discusses the Insert New Object dialog box. >>


Change Icon dialog box

<< Write a topic here that discusses the Change Icon dialog box. >>


Convert dialog box

<< Write a topic here that discusses the Convert dialog box. >>


Paste Special dialog
Paste Special dialog box

<< Write a topic here that discusses the Paste Special dialog box. >>


Update command
Update command (File menu)

<< Write a topic here that discusses the Update command. >>


Save Copy As... command
Save Copy As... command (File menu)

<< Write a topic here that discusses the Save Copy As... command. >>


Embedded Object Resize Bar

<< Write a topic here that discusses the embedded object resize bar. >>


Manual Overview

This is the entry point for the Diamond online user manual, which substitutes a printed user manual.

The manual offers the following chapters:

Desktop

Working With Diamond

Files

Editing of Structural Data

Building up Structural Parts

Display of Structure Picture

Distances and Angles

Info Mode

Printing, Copying, and Saving the Structure Picture

Data Sheet


The Diamond Desktop: Overview

This chapter informs you about the components of the Diamond screen, such as menus, toolbars etc.

You should use DIAMOND with a screen resolution of 1024 x 768 pixels or more to get the maximum functionality, although the lower resolution of 800 x 600 pixels is rather acceptable, but keep in mind that toolbars and big dialog boxes will hide most parts of the structure window. Lower resolutions (e.g. the VGA standard resolution of 640 x 480 pixels) should never be used, since some dialog boxes are wider than 640 and higher than 480 pixels.

You should also use a color resolution with more than 256 colors, that means "High Color" (32,768 or 65,536 colors) or better "True Color" (16.7 millions of colors) for better graphical results.

The following articles inform you in details about:

•	Opening and closing of structure windows,

•	the different parts ("panes") of the structure window,

•	the menu bar and local popup menus,

•	toolbars,

•	the status bar.


The Diamond Desktop: Opening and Closing of Structure Windows

DIAMOND is supplied with the so-called "Multiple Document Interface" (MDI), where each document contains one (crystal) structure dataset. You can open as many structure windows as much memory (and room on the screen) is available. That means if you open a new structure window or an existing structure file, the contents of the structure window you just have been processing, will not be discarded.

You can arrange the structure windows using the appropriate commands from the "Window" menu. There are additional commands in the system menu of each structure window (in the left corner of the structure window's titlebar) to maximize or minimize (iconize) a window.


The Diamond Desktop: Panes

The Diamond structure window consists of two different parts, called "panes", the main pane which displays the structure picture, and a secondary pane on the right that displays textual information such as a data sheet, lists of atoms or distances and angles. The main pane is often called "graphics pane", whereas the secondary pane is often called "data pane".

The following types are used for the secondary pane, most of them are object lists:

•	The list of atoms in the parameter list;

•	the list of created atoms;

•	the list of created bonds;

•	the list of atom types;

•	the list of bond types;

•	the list of coordination polyhedra;

•	the list of distances and/or angles;

•	the data sheet, which displays structural parameters as well as bibliographic data;

This example shows the main pane containing the structure picture and (on the right) the list of created atoms sorted for atom symbols and with "Ag(3)" highlighted.

Main pane and secondary pane are divided by a so-called "splitter", which can be shifted by dragging with the mouse, e.g. like the splitter between the tree view (left part) and the list view in the MS Windows Explorer.

You can activate a pane by clicking into it with the mouse or by using the hotkey F6 which is common to MS Windows application using different panes.

Normally the secondary pane is hidden, but can be opened via the appropriate command at the bottom of the "Display" menu. Use the mouse to drag the splitter to the desired position.

The secondary pane can be closed by dragging the splitter to the rightmost position of the structure window.

The width of the main pane as well as the type of secondary pane will be saved in the Diamond configuration file when a structure window or a Diamond session is closed, so that it will appear at the same position if a new structure window is opened or if a new Diamond session is started.


The Diamond Desktop: Menus

Like most MS Windows application, Diamond has a menu bar below the title bar. Diamond uses two different menu bars:

•	The regular menu bar if at least one structure window is open and

•	the short menu bar if no structure window is open.

To activate the menu use the left mouse button and click on an available entry. Alternatively press the Alt key, choose the appropriate entry using the cursor keys, and then press Enter. Some menu entries may be parents of another menu, a so-called "submenu".

This example shows the "Structure" menu, with the opened submenu of the "Fill" command. Note the brief help text in the status bar at the bottom of the Diamond application window.

Additionally local popup menus are available. You can open such a popup menu either

•	by clicking with the right mouse button or

•	by using the keyboard (Shift+F10 or the special context menu key on a Windows 95 keyboard)

These popup menus are context-sensitive and depend on the pane you are working with or you have clicked into and eventually the object you have selected.

Please note that not all functions in the menus are available at the same time, e.g. the command to create a molecule will be disabled if no atom has been defined in the parameter list.

This example shows the context menu for a selected atom, which offers you a collection of the most important commands for the selected object (here: for the atom). Note that not all commands are available at that time.


The Diamond Desktop: Toolbars

A toolbar is a control bar which contains a row of button images, often called "icons". These buttons represent a lot of functions which are also available via menu commands, such as "New", "Open", or "Save". Additionally they contain buttons for commands that you else would reach only indirectly (e.g. via dialog boxes).

Toolbars are usually aligned to the top of the Diamond application window, that means below the menubar. But the toolbars used in Diamond can be “docked” to any side (or sides) of the Diamond application window. They can also be made to “float” in draggable “mini-frame windows”, and you can now resize floating toolbars.

Diamond offers you five different toolbars:

•	The "Standard" toolbar for standard command such as "New", "Open", "Copy" etc.

•	The "Display" toolbar for the most common commands for the representation of the structure picture.

•	The "Build" toolbar for the most common commands for building up structural parts.

•	The "Tracking" toolbar to switch between tracking modes.

•	The "Measure" toolbar for the interactive measuring of distances or angles.

The following screenshot gives you an overview how toolbars can be arranged:

In this example, both Standard and Display toolbar are aligned to the top of the application window. The Build toolbar is aligned to the left, the Tracking toolbar to the bottom of the application window. The Measure toolbar is "floating" on the structure window.

You can shift, dock or "undock" a toolbar by dragging the corresponding toolbar with the left mouse button. You can also switch between docked and floating state by double-clicking into the interior of the toolbar (but outside the buttons on the toolbar).

You can hide and re-display toolbars via the Toolbars command from the Display menu.


The Diamond Desktop: Status Bar

The status bar is a control bar with a row of text output panes, or “indicators”, at the bottom of the Diamond application window. The main part (beginning at the left) displays either result messages or brief help for the menu or toolbar command where the mouse cursor is just pointing to.

During lengthy processes, such as filling of larger cell ranges or displaying a rendered picture with some hundreds of atoms, the progress of the operation will be displayed, like in the following example:

At the right end of the status bar, four panes, called "indicators", show the actual number of:

•	atoms in the parameter list,

•	created atoms,

•	bonds between created atoms,

•	and coordination polyhedra.

Whenever a progress bar is displayed in the status bar, the corresponding operation (e.g. filling a cell range or creating an enhanced picture) can be cancelled by pressing the Ctrl+Break key combination.


Working With Diamond: Overview

Although Diamond is a typical MS Windows application and uses as much as possible handling like in other, common MS Windows applications, there are some important notes that distinguishes the handling of Diamond from that in other applications.

Like in most other typical MS Windows applications, Diamond uses:

•	The Multiple Document Interface (MDI) that allows to work with different structure documents independent from each other.

•	Common "hotkeys" for common file operations, selecting etc. For example: Ctrl+N to open a new structure document, Ctrl+O to open an existing document, Ctrl+F6 to change to the next open structure document (next window), Ctrl+A to select "all" (all objects of the structure picture, all items in a list, etc.), and many other more.

•	Context-sensitive help is available when you press the F1 key when a dialog box is open or a menu item is highlighted. In addition to this help on demand, Diamond offers a special mode, the "Info mode". For details, see "Context-sensitive Help".

•	Selection of objects. The objects of the structure picture may particularly be compared with objects in a 2D or 3D graphics application. Objects may be selected by clicking on. Selections may be inverted by clicking on it with the Shift key pressed down, etc. For details, see "Selecting Objects".

•	An "Undo" function which allows you to cancel the latest operation that may have changed the structure document. In Diamond, this function works with multiple steps. That means, with every call to the Undo function, you restore the latest state of the document, then the state before that change, etc. backwards. Vice versa, this multiple-step restoring may be restored, which is called the "Redo" function. For details, see "Undo and Redo".


Working With Diamond: Context-sensitive Help

This article describes, where and how context-sensitive help is available for the several working situations in your Diamond session.

Pressing F1 key

If neither a dialog box is open nor a menu item is highlighted, pressing of the F1 key opens the "Diamond Help Index", a general page with an introduction to the Diamond Help Library.

If a menu item is highlighted, help for that menu item (usually command) will be displayed. The menu item may be highlighted using the mouse or with the cursor keys.

If a dialog box is open, F1 will show specific help for the usage of that dialog and the meaning of the controls in the dialog box.

Entering Help Mode

A special mode, the "Help mode", is activated by either pressing the Shift+F1 key combination, or by clicking on the [image] button in the standard toolbar. This is a more versatile method of getting context-sensitive help. After this mode has been activated, the mouse cursor changes to a symbol consisting of standard arrow and question mark. In this mode, you will get context-sensitive help, if you click on a menu item or a symbol in a toolbar or on special parts of the Diamond application window, such as the status bar, system menu etc.

The Help mode can be cancelled by pressing the Esc key. The previous mouse cursor will be restored. The Help mode ends automatically, when you get help for a clicked item.

Info Mode

Whereas the previously described Help mode is common to many other MS Windows application, a special mode offering informations about objects of the Diamond structure picture is available by pressing the [image] button in the standard toolbar, or by choosing the Info mode command from the Tools menu.

When this mode is activated, the mouse cursor changes to an arrow with an "i" letter. This mode can be cancelled by pressing the Esc key or by pressing the [image] button again or by choosing the Info mode again from the Tools menu. The previous mouse cursor will be restored.

For details about this mode, see the article "Info Mode: Overview".


Working With Diamond: Selecting Objects

This article describes, how objects of the Diamond structure picture (that means, atoms, labels, etc.) can be selected.

The following object types of the structure picture can be selected. The table lists how an object is selected by clicking into an object-dependent 2D range within the structure picture.

Atom	Click into the rectangle that surrounds the atom. In standard representation using no ellipsoids, this is a square with the radius of the atom. In ellipsoid representation, it is the rectangle which surrounds the ellipsoid projection completely.
Polyhedron	A polyhedron is selected by its corresponding central atom.
Bond	Click on the bond. The marker of the bond is the rectangle surrounding the 2D projection of the bond completely.
Atom or bond label	Click into the surrounding rectangle of the label.
Text	Click into the surrounding rectangle of the user-defined text.
Coordinate system	Click into the rectangle that surrounds the coordinate system which symbolizes the current orientation.
Legend	Click into the rectangle of the legend of atom types.

Standard selection

The most common way to select an object is to move the mouse cursor to a suitable position of the object (see table above) and then click the left mouse button. The selection is reflected by a rectangle which surrounds the selected object. All other selections will be restored in that moment.

Extended selection

If you hold down the Shift key when you click on an object, the selection of that object will be inverted independent from the selection state of all other objects in the structure picture. Usually the auxiliary Shift key is used to select multiple objects that cannot be "catched" with a rectangle (see below). That means, object at different positions may be clicked and selected one after the other.

Rectangle selection

If you press down the left mouse button outside of an object, then pull up a rectangle by moving the mouse cursor with left mouse button down, and then release the button, you will select all objects that lie completely inside that rectangle. You can additionately press the Shift key to invert the selection of all objects in the rectangle (combination of extended and rectangle selection).

Temporarily hiding of objects

You can hide objects of selected types temporarily for a better access to other objects. For example, it is easy to select atoms that are covered by labels or to access polyhedra by their associated central atoms when the polyhedron faces are closed. To hide objects temporarily, choose the Hide command from the Display menu. Please note that the objects will not be discarded, and the hiding is not stored in the structure document.

Indirect selection with auxiliary object lists

You can select objects of the structure picture by selecting the corresponding items in the lists that can be displayed in the secondary pane (text pane). To open a list in the text pane, choose the corresponding command from the submenu which opens when you choose the List command from the Display menu.

If the list of created atoms is displayed in the text pane, the selection of each atom in the structure picture is reflected in the atom list. On the other hand, you can change the selection of the atoms in the picture by changing the selection of the corresponding items of the atom list. That means, by sorting the atom list in a suitable way, you have varied possibilities to select a very special portion of the atoms in the picture.

Like atoms, bonds can be selected from the bond list. For example, if you sort the bonds in the list for bond lengths, you can select all bonds with lengths within that given range.

Polyhedra (that means, the corresponding central atoms) can be selected with the help of the polyhedra list.

The lists of atomic parameters, atom types, and bond types offer enhanced features to select atoms and bonds, rsp. For example, if you want to select all atoms that have been created from a special atom of the parameter list (e.g. all symmetry-equivalent atoms of "Fe 3"), first select the atom in the parameter list, and then choose the Select atom(s) command from the context menu of the atomic parameter list. The atom type list and the bond type list can be used to select all atoms and bonds, rsp., that belong to the selected atom type(s) and bond type(s), rsp.

Commands for selection

To select a complete molecule, select an atom of the molecule, and choose the Select molecule command from the context menu.

To select all objects of the structure picture, choose the Select all command from the Edit menu or simply use the "hotkey" Ctrl+A.

To invert the current selection, choose the Invert selection command from the Edit menu or simply use the "hotkey" Ctrl+I. This command can be used to select all but one molecule, for example.


Working With Diamond: Undo and Redo

Diamond has a multiple-step Undo function, which means that each time a structure document may change, the previous state is saved temporarily. The Undo buffer works with the "Last in - First out" principle. You can call the Undo function and restore previous states of the document stepwise until the bottom of the Undo buffer is reached. The bottom is the state where the document has been created (new document) or has been loaded or imported from an existing file. The action that will be restored is described in brief after the Undo command in the Edit menu, for example "Undo: Fill unit cell	Ctrl+Z".

The restoring of a previous state may be restored in the same way, using the "Redo" function. In that case, you work to the top of the Undo buffer. Like for Undo, the action that will be "re-restored" is described in brief after the Redo command in the Edit menu.

Diamond offers several possibilities to work with the Undo/Redo buffer:

Undo:

•	Choose the Undo command from the Edit menu.

•	Or click on the [image] button in the standard toolbar.

•	Or press the Ctrl+Z key combination.

Redo:

•	Choose the Redo command from the Edit menu.

•	Or click on the [image] button in the standard toolbar.

•	Or press the Ctrl+Y key combination.

Remarks

The "Undo" and "Redo" functions refer to the structure in the currently active structure window only! Example: If you first change structure A and then focus the picture of structure B, the "Undo" or "Redo" function applies to structure B ! That means you cannot restore any changes of structure A as long as structure B is focussed and not until structure A is activated again.

You cannot restore any changes to a structure after its corresponding structure window has been closed.

Neither closing nor saving of structural data can be restored. But you may undo the last operations and then save the restored state.


Files: Overview

This article gives you an overview what kind of structural data can be read by Diamond in which form.

The native data format that is used by Diamond version 2.0 and higher is the so-called "Diamond Structure File" format. The files have the extension ".DSF". Although the older version 1.x of Diamond used the same file extension, old and new DSF format are quite indifferent. See the articles "Diamond Structure File Format (DSF 2)" and "Compatibility with Diamond 1.x File Format" for more details about the Diamond file formats.

Both Diamond's native data as well as foreign formats are opened in principally the same way. The automatic file type recognition of Diamond decides whether the structural data need to be converted. For details which foreign file formats are supported by Diamond in what way, see the article "Importing Foreign File Formats". For more informations how files can be opened in Diamond, see "Opening Structure Files".

If a data file contains descriptions of more than one (crystal) structure only, a list of all descriptions in that file is offered, where you can select one or more structures to open. Read the article "Multiple Structure Descriptions in One File" how to proceed.

Files in selected directories can be searched for specified structural data, such as bibliographic data, chemical composition, and many more. See the article "Searching Structure Files", how this can be done.

The articles "Saving Structural Data" and "Exporting Structural Data to Foreign Formats" describe how structural data are saved - normally in the Diamond native format, or "exported" to another file format.

Read the articles "Auto Save Function" and "Temporary Files", if you want informations about temporary file management of Diamond.


Files: Diamond Structure File Format (DSF 2)

The native structure file format used by Diamond version 2.0 or higher is the "Diamond Structure File" format (DSF 2). This format is binary, which means that it cannot be read by a text processor like CIF format.

Please note: The DSF 2 format is the only file format that can store all kind of data entered or changed in a Diamond session, whereas the other file formats supported by Diamond usually store structural parameters and some textual data only.

Files with the extension DSF are treated automatically as Diamond Structure Files, since Diamond has registered this file type on your MS Windows 95 or NT machine. Thus Windows recognizes a DSF file as "Diamond Document" and starts Diamond automatically when you double-click on a DSF file, e.g. in the Windows Explorer.


Files: Importing Foreign File Formats

Foreign files are opened in principally the same way as native Diamond structure files. That means, there is no separate "Import" command like in some other competitive applications. Moreover, Diamond recognizes the format automatically and creates a temporary DSF 2 file (as copy) from the original file, where it reads data from later.

Read the article "Opening Structure Files" about several ways to open a structure file.

If the file contains one structure description only, a structure window will be created for that structure automatically. If there are multiple structure descriptions, a list of all entries in the file will be displayed, where you can select one or more structures from. For details, see the article "Multiple Structure Descriptions in One File".

Foreign file formats supported by Diamond 2 and how they are recognized

The following file formats can be recognized and read by Diamond 2:

Diamond 1.x format

This format is binary like DSF 2, but uses a quite different format than Diamond 2, and is thus treated as a "foreign" format like the other formats below. You may get informations about the compatibility with DSF 1 format from the article "Compatibility with Diamond 1.x File Format". The DSF 1 format is recognized by its special header.

Crystallographic Information File (CIF)

This free text format is recognized by a line beginning with "data_", e.g. "data_global" or "data_cstio3".

CRYSTIN Download format

This text format is created by the retrieval system of the Inorganic Crystal Structure Database (ICSD) and is recognized by a line beginning with " 0000", which signs the beginning of the first or the next entry, rsp.

Cambridge Structural Database (CSD) FDAT format

This text format is created by the retrieval system of the Cambridge Structural Database (CSD) with the "SAVE 3" command and is recognized by a line beginning with "#" followed by the CSD Reference Code, which signs the beginning of the first or the next entry, rsp.

Brookhaven Protein Data Bank (PDB) format

This text format may be created from the browser of the Protein Data Bank (PDB) and is recognized by the "HEADER" statement signing the beginning of the PDB entry.

SHELX-93 format

To recognize this text format, Diamond searches for a line beginning with "CELL", which indicates wave length and the cell parameters a, b, c, alpha, beta, and gamma.

XYZ format

This text format is recognized as XYZ format, if the first line contains a number and the third line consists of element symbol plus three floating point numbers.

Data items read from a Crystallographic Information File

You can get informations about the Crystallographic Information File (CIF) format from the World-Wide Web site of the International Union of Crystallography (IUCr) in Chester, U.K. The original paper describing the CIF standard has been published in Acta Cryst. (1991). A47, 655-685. The latest core dictionary is available from http://www.iucr.org/cif/cif_core/index.html.

The following CIF data items are evaluated by Diamond 2:

CIF data item	Comment
_atom_site_aniso_label	This symbol is used to identify an atom in the parameter list.
_atom_site_aniso_U_11, etc.	The anisotropic displacement parameters of type U, given in Angstroems squared.
_atom_site_aniso_B_11	dito for type B.
_atom_site_attached_hydrogens	The number of hydrogen atoms attached to the atom at this site excluding any H atoms for which coordinates (measured or calculated) are given.
_atom_site_calc_flag	"d": this site has been determined from diffraction measurements; "calc": this site has been calculated from molecular geometry; "dum": dummy site with meaningless coordinates.
_atom_site_fract_x, _atom_site_fract_y, _atom_site_fract_z	The coordinates of the atom site as fractional coordinates x/a, y/b, and z/c, that means relative to the axes of the unit cell.
_atom_site_label	The label (that means identifier) of the atom site.
_atom_site_occupancy	The fraction of the atom present at this site.
_atom_site_symmetry_multiplicity	The multiplicity of the site.
_atom_site_thermal_displace_type	A standard code used to describe the type of atomic displacement parameters used for this site: Diamond accepts the following codes: "Bani" for anisotropic displacement parameters of type B, "Uani" for anisotropic displacement parameters of type U, "Biso" for an isotropic or equivalent displacement parameter of type B, "Uiso" for an isotropic or equivalent displacement parameter of type U.
_atom_site_type_symbol	The symbol of the corresponding atom type. This symbol must occur in the atom type loop.
_atom_site_U_iso_or_equiv	The isotropic displacement parameter, or the equivalent displacement parameter calculated from anisotropic displacement parameters, with units in Angstroems squared.
_atom_site_Wyckoff_symbol	The Wyckoff letter of the site.
_atom_type_oxidation_number	The formal oxidation state or charge of the corresponding atom type, which has usually been defined previously in the atom type loop.
_atom_type_radius_bond	The effective radius of the corresponding atom type.
_atom_type_symbol	The symbol of an atom type. This symbol may be used in the atom site loop to reference the atom type from the atomic parameter list.
_audit_creation_date	A date that the CIF is created, with format yy-mm-dd.
_audit_creation_method	A description of how data was entered into the CIF. This is treated as simple text.
_audit_update_record	A record of any changes to the CIF. Only the date (format yy-mm-dd) will be read by Diamond, but not the description of changes, which may follow the date.
_cell_angle_alpha, _cell_angle_beta, _cell_angle_gamma	The unit cell angles alpha, beta, and gamma in degrees. Standard uncertainties will be accepted by Diamond.
_cell_formula_units_Z	The number of formula units in the cell. This value is treated as integer number.
_cell_length_a, _cell_length_b, _cell_length_c	The lengths of the unit cell axes a, b, and c in Angstroems.
_cell_volume	The volume of the unit cell in cubic Angstroems. This value will be overwritten, since Diamond calculates the cell volume from the cell parameters.
_chemical_compound_source	The source of the compound, which will be treated as simple text.
_chemical_formula_analytical	The analytical formula which may contain traces of elements not mentioned in the atomic parameter list. This kind of formula is treated as text and not evaluated by Diamond and not compared with the atomic parameter list.
_chemical_formula_structural	The structural formula, which is treated as text and not evaluated by Diamond and not compared with the atomic parameter list.
_chemical_formula_sum	The formula sum, which should agree with the atomic parameter list. This data will be read by Diamond, but overwritten there by the calculated formula sum.
_chemical_formula_weight	The formula mass in daltons.
_chemical_formula_weight_meas	The formula mass in daltons measured by a non-diffraction experiment.
_chemical_melting_point	The melting point of the crystal in Kelvin.
_chemical_name_mineral	The mineral name.
_chemical_name_structure_type	The name of the structure type.
_chemical_name_systematic	The IUPAC or Chemical Abstracts full name of the compound.
_database_code_CAS	The Chemical Abstracts Code.
_database_code_CSD	The "Reference Code" of the Cambridge Structural Database (CSD).
_database_code_ICSD	The "Collection Code" of the entry in the Inorganic Crystal Structure Database (ICSD).
_database_code_MDF	The reference code of the "CRYSTMET" Metals Data File.
_exptl_crystal_density_meas	Density value measured using standard chemical and physical methods, in grams per cubic centimeter.
_geom_angle	An angle in degrees bounded by the corresponding site labels. The apex of the angle is at site label #2.
_geom_angle_atom_site_label_1, _geom_angle_atom_site_label_2, _geom_angle_atom_site_label_3	The atom site labels of the three atoms which define the angle specified by "_geom_angle", where "_geom_angle_atom_site_label_2" specifies the atom at the apex of the angle.
_geom_angle_publ_flag	This code signals if the angle is reffered to in a publication of should be placed in a table of significant angles ("yes" or "no").
_geom_angle_site_symmetry_1, _geom_angle_site_symmetry_2, _geom_angle_site_symmetry_3	The symmetry code of the atom #1, #2, and #3, rsp., that define the angle.
_geom_bond_atom_site_label_1, _geom_bond_atom_site_label_2	The atom site labels of the two atoms that form a bond.
_geom_bond_distance	The bond length in Angstroems.
_geom_bond_publ_flag	This code signals if the bond distance is referred to in a publication of should be placed in a list of special bond distances ("yes" or "no").
_geom_bond_site_symmetry_1, _geom_bond_site_symmetry_2	The symmetry code of the atom #1 and #2, rsp., that define the bond distance.
_geom_contact_atom_site_label_1, etc.	Diamond treats the items beginning with "_geom_contact..." like bonds, that means like the corresponding items beginning with "_geom_bond...".
_geom_torsion	The torsion angle in degrees bounded by the corresponding four atom sites. The torsion angle definition should be that of Klyne, W. & Prelof, V. (1960). Experientia, 16, 521-528.
_geom_torsion_atom_site_label_1, _geom_torsion_atom_site_label_2, _geom_torsion_atom_site_label_3, _geom_torsion_atom_site_label_4	The atom site labels of the four atoms that define the torsion angle. The vector direction from atom #2 to #3 is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector site 2 - site 1 onto the projection of the vector site 3 - site 4. Clockwise torsions are positive, counterclockwise torsions are negative.
_geom_torsion_publ_flag	This code signals if the torsion angle is referred to in a pub lication of should be placed in a list of special torsion angles ("yes" or "no").
_geom_torsion_site_symmetry_1, _geom_torsion_site_symmetry_2, _geom_torsion_site_symmetry_3, _geom_torsion_site_symmetry_4	The symmetry code of the atom #1, #2, #3, and #4, rsp., that define the torsion angle.
_journal_coden_ASTM	The ASTM journal coden of the publication.
_journal_page_first, _journal_page_last	The first and last page of the publication. These values are treated as text instead of numbers, since they may contain extensions like "255A".
_journal_volume	The volume of the publication, treated as text.
_journal_year	The year of the publication. If it is less than 100, 1900 will be added.
_publ_author_name	The name of the author or the name of one of the authors.
_publ_section_comment	A comment which usually consists of multiple lines.
_publ_section_title	The title of the publication.
_refine_ls_R_factor_all	Residual factor for all reflection data.
_refine_ls_R_factor_obs	Residual factor for reflection data classified as "observed".
_symmetry_cell_setting	The cell settings for the space group symmetry of the entry, which is used to supplement missing cell parameters. This can be one of the symbols "triclinic", "monoclinic", "orthorhombic", "tetragonal", "rhombohedral", "trigonal", "hexagonal", and "cubic".
_symmetry_equiv_pos_as_xyz	A symmetry matrix in the "x,y,z" format, including those for lattice centring and centrosymmetry, if present.
_symmetry_int_tables_number	The space group number from the International Tables for Crystallography, Vol. A.
_symmetry_space_group_name_Hall	The Hall space group symbol (compare Hall, S. R. (1981). Acta Cryst. A37, 517-525).
_symmetry_space_group_name_H-M	The Hermann-Mauguin space group symbol.

Data read from the CRYSTIN Download format

A "CRYSTIN Download" file can contain multiple structure descriptions, usually of entries of the Inorganic Crystal Structure Database (ICSD). Diamond reads the following data from each entry of the file. (This information is taken from the ICSD-CRYSTIN user's manual, by G.Bergerhoff, B.Kilger, C.Witthauer, R.Hundt, R.Sievers, Institut fuer Anorganische Chemie der Universitaet Bonn, 1986):

1st record of every entry:

 Byte

 1- 8  ' 0000   ' Record label

 9-14  Collection code

15     free

16-21  Relative entry number

22-80  free

This  record  is followed by other records with various formats,

according to the selected categories.

Categories with unstructured text:

 Byte

 1     free

 2- 3  figures according to the categories:

        1 - NAME (N) Compound name

        2 - RFCD (V) Refcode (only in CCDF)

        3 - MINR (M) Mineral name

        4 - FORM (F) Chemical formula

        5 - TITL (T) Title of publication

        7 - AUT  (A) Author's name

        9 - SGR  (R) Space group symbol after Hermann-Mauguin

       16 - REM  (Z) Additional remarks

       19 - PICT (K) Information to produce a drawing in

                     optimized view

 4     0

 5     Number of continuation records. 0 if the text contains

       less than 73 characters.

 6- 8  free

 9-80  Text. After each 72 characters a continuation record is

       used.

Category REF (Q):

  Byte

  1- 8  '  600   ' Record label

  9-10  Year of publication

 11-15  CODEN

 16-22  Volume

 23-29  First page

 30-36  Last page (in CCDF: repetition of first page)

 37     free

 38     Character (if the page numbers consist of figures

        with a preceding alphabetic character);

        otherwise free

 39-42  Issue, if necessary. Otherwise 0.

Category CELL (E). Missing fields are indicated by -1.0.

Standard deviations are given in an absolute scale.

 Byte

 1- 3  '  800   ' Record label

 9-17  a (A)

18-25  Sigma(a)

26-34  b (A)

35-42  Sigma(b)

43-51  c (A)

52-59  Sigma(c)

60-66  Alpha (degrees)

67-74  Sigma(alpha)

75-80  free

 Byte

 1- 3  '  810   ' Record label

 9-15  Beta (degrees)

16-23  Sigma(beta)

24-30  Gamma (degrees)

31-38  Sigma(gamma)

39-41  Number of formula units

42-47  Measured density

48-55  Sigma(density)

56-66  Unit cell volume (A**3)

67-80  free

Category SYM (S):

 Byte

 1- 8  ' 100   ' Record label

 9-16  1st line of symmetry matrix

17-24  2nd line

25-32  3rd line

33-80  free

Category PARM (P):

 Byte

 1- 8  ' 1200   ' Record label

 9-10  Atomic symbol

11-13  Number

14-19  Oxidation state

20-22  Number of positions. In CCDF: Multiplicity of

       the general position.

23     Wyckoff symbol

24-31  x

32-39  Sigma(x)

40-47  y

48-55  Sigma(y)

56-63  z

64-71  Sigma(z)

72-80  free

 Byte

 1- 8  ' 1210   ' Record label

 9     Type of temperature factor (B, U, A or L)

 10-20 Isotropic temperature factor if byte 9 is B oder U

 21-29 Standard deviation of isotropic temperature factor

 30-36 Site occupation, related to the multiplicity of the

       special position

 37-44 Standard deviation of the site occupation

 45    Number of non-located hydrogen atoms (H or D) bonded

       to the atom

 46    H or D, if byte 45 is not 0

 47-80 free

Categories BETA (B), BIJ (C) or UIJ (D):

 Byte

 1- 8  ' 1300   ' = Temperature factor type "Beta(i,j)"

       ' 1400   ' = Type "B(i,j)"

       ' 1500   ' = Type "U(i,j)"

 9-10  Atomic symbol

11-13  Number

14-24  Factor (1,1)

25-33  Sigma

34-44  Factor (2,2)

45-53  Sigma

54-64  Factor (3,3)

65-73  Sigma

74-80  free

 Byte

 1- 8  ' 1310   ' = Temperature factor type "Beta(i,j)"

       ' 1410   ' = Type "B(i,j)"

       ' 1510   ' = Type "U(i,j)"

 9-19  Factor (1,2)

20-28  Sigma

29-39  Factor (1,3)

40-48  Sigma

49-59  Factor (2,3)

60-68  Sigma

69-80  free

Category RVAL (I):

 Byte

 1- 8  ' 1800   ' Record label

 9-17  R value

18-80  free

Category TEST (Y):

 Byte

 1- 8  ' 2000   ' Record label

 9-10, 11-12, 13-14 etc.: Code figures

Category SMAT:

 Byte

 1- 4  ' 240' Record label

 5- 6  Number of SMAT Records which follow immediately

 7- 8  free

 9     Keys for the Bravais translations:

       0 = P     3 = B     7 = R (obverse)

       1 = F     4 = C     8 = R (reverse)

       2 = A     5 = I    (7 or 8 only for space

                           groups in hexagonal setting)

10     free

11-18  t1

19-22  r12

23-26  r13

27-30  r14

31-38  t2

39-42  r21

43-46  r22

47-50  r23

51-58  t3

59-62  r31

63-66  r32

67-70  r33

71-73  Space group number (Int. Tables) or 0

Data read from a SHELX file

The following data are read from a SHELX file:

TITL	The title for the structure (maximum 76 characters)
CELL	The first parameter is the wavelength and is overridden; the following six parameters are the cell parameters a, b, c, alpha, beta, and gamma in Angstroems and degrees, rsp.
ZERR	The standard uncertainties of the values given in "CELL". Only the standard uncertainties of the cell parameters are read by Diamond.
LATT	The absolute value of the LATT parameter defines the lattice centering, the sign the presence (+) or absence (-) of centrosymmetry.
SYMM	The symmetry matrices. A space group symbol is not given in a SHELX file. Diamond evaluates the space group of the compound from the symmetry matrices and the LATT parameter.
SFAC	These parameter(s) are used to assign the atoms of the parameter list to atom types (elements).
END	Defines the end of the structure description.

Other data items, such as UNIT, AXIS, etc. are not read by Diamond. If the first four character of a line do not represent a SHELX keyword, this line will be interpreted as atom description, whereas four blanks define a comment.

Atomic parameters

Diamond reads at least four parameters following the atom symbol. The first parameter is used to derive the element symbol from the previous SFAC definitions. The following parameters are the x, y, and z value of the atomic position in fractional coordinates. These parameters may be followed by the site occupation factor, the isotropic or equivalent displacement parameter of type U, or the six values of the anisotropic displacement parameters of type U.

Data read from CSD FDAT format

A file in the FDAT format of the Cambridge Structural Database (CSD) may contain multiple entries. The '#' character followed by a maximum of eight characters or digits at the beginning of a line defines the entry point of the first or a following structure description.

The characters #2 through #9 are taken as CSD Reference Code (the first character of a line has number #1). The following informations of the first line of an entry will be read:

•	The recording date of the entry, which has the format "yymmdd".

•	The year of the publication of the entry, which has two digits only.

The following line, which is not mandatory in CSD FDAT format, contains the cell parameters and space group information:

•	The cell parameters a, b, c, alpha, beta, and gamma in Angstroems and degrees, rsp.

•	The standard uncertainties of the cell parameters.

•	The measured density in grams per cubic centimeter.

•	The space group number according to International Tables for Crystallography, Vol. A.

•	The Hermann-Mauguin space group symbol.

•	The number of formula units per unit cell.

The following line(s) define several numeric and text fields:

•	The R value.

•	Remarks including "Disorder field" and "Error field".

The next lines contain the coded symmetry matrices, if symmetry information is given.

If radii are given in the CSD FDAT file, these values will be read from the following line. These definitions consist of pairs of element symbol and radii in picometers. These values will be used as effective radii for the atom type definitions in Diamond.

For each atom in the parameter list only element symbol and the coordinates x, y, and z are given. These coordinates are fractional, unless no cell parameters have been defined.

Bond distances will be ignored.

Bibliographic informations

When converting a CSD FDAT file, Diamond searches for a file with the same name of the FDAT file but with the extension JNL, to retrieve additional bibliographic informations:

•	The name of the compound.

•	The structural formula.

•	The name(s) of the author(s).

•	The citation.

Data read from a PDB file

The first line of a Protein Data Bank (PDB) file begins with "HEADER". From the first line, also the recording date of the PDB entry as well as the database code are read.

The following table lists the keywords that are interpreted by Diamond when reading from a PDB file:

TITLE	The title of the compound or of the publication.
COMPND	This will be used as common name.
SOURCE	The source of the compound.
REVDAT	The revision date will be used as last update of the database entry.
JRNL	Retrieves data that specify a publication of the database entry. The sub-keywords "TITL", "AUTH", "REFN", and "REF" are used to specify the title, the authors' names, and the citation.
CRYST1	Defines the cell parameters a, b, c, alpha, beta, and gamma in Angstroems and degrees, rsp.
SCALE1, SCALE2, SCALE3	Define the three rows of a transformation matrix, which transforms the coordinates of the atomic parameters from cartesian back to fractional coordinates.
ATOM, HETATM	Define an atom. Diamond does not distinguish between "normal" atom and hetero atom. From an ATOM or HETATM record, Diamond extracts the atom symbol (which contains the element symbol), the coordinates x, y, and z, which are given as cartesian coordinates (in Angstroem units) and are transformed to fractional coordinates, the site occupation factor and the isotropic or equivalent displacement parameter of type U. Newer entries may have the oxidation number defined in one of the last columns of an atom record.
SIGATM	The standard uncertainties of the corresponding fields of an atom or hetero atom record.
ANISOU, SIGUIJ	The six anisotropic displacement parameters of type U and their standard uncertainties.
END	Signals the end of the database entry.

Data read from the XYZ format

The XYZ format is rather simple. The contents of the second line is treated as title. The following lines are atomic parameters containing element symbol and cartesian coordinates x, y, and z.


Compatibility with Diamond 1.x File Format

Version 2.0 or higher of Diamond uses a file format which is different from that format used by version 1.x of Diamond (DSF 1 format).

Since there are some new options in Diamond 2.0 such as rendered representation, the new file version can store more information than the older file version. In other words, the new file version can store every data that can be stored in the old file version, but not vice versa. That means, if you open an old Diamond 1.x file, some settings become default settings (like the ones for rendered representation). If you save a structure document in the old file format, these settings will get lost. (Only with the Diamond 2.0 format, you can store every data you have edited with Diamond version 2.0.)

The following table will show you where Diamond uses default settings if you open a file that has been created with Diamond 1.x - and where data would be dismissed, if you save data from a Diamond 2.0 document in the old file format.

Rendered representation

Since Diamond 1.x uses no rendered representation for the structure picture, there are no items for light properties, material properties, transparency, etc. in the DSF 1 format. When converting to DSF 2 format, default settings will be used. The default settings are described in the article "Rendered Representation: Overview".

Designs of atoms in the structure picture

Diamond 2 uses three different colors (interior color, edge color, pattern color) for an atom, whereas Diamond 1.x uses one main color and some few options for a "secondary color". The radius of every atom can be changed individually in Diamond 2, whereas Diamond 1.x uses the radius which has been defined for the corresponding atom type.

Designs of bonds

Diamond 2 uses two different colors (interior color, edge color) for thick bonds, which are represented as tubes or truncated cones, whereas Diamond 1.x uses one main color and some few options for a "secondary color" (compare atom designs).

Atom and bond labels

Diamond 2 uses a third coordinate (z) for the distance between label and object reference point (e.g. the center of the atom), which is necessary for rendered representation. When converting label data from DSF 1 format, Diamond 2 sets the z-value to 0.5 (Angstroems) to avoid that the label text penetrates the atom sphere.

There is no limitation for the label distance (+/-1.27 Angstroems from the reference point in Diamond 1.x) in DSF 2 format.

In Diamond 2, every single label can have its own color, whereas DSF 1 offers two choices only: one color for all labels, or each label has the same color as the corresponding atom or bond.

Polyhedra

Since no material properties are defined for polyhedron faces in DSF 1 format, there is no transparency. Transparency will be set to zero, when DSF 1 data are converted to DSF 2 format, which results in opaque polyhedron faces.

Limitations for bibliographic data

The sum of the lengths of all bibliographic texts must not exceed 65,532 bytes in DSF 1 format, whereas DSF 2 has no restrictions for that.


Files: Opening Structure Files

Diamond offers several ways to open a structure file, independent from its file format:

Using the File Open dialog

The usual way to open a file in Diamond - as in common MS Windows applications - is to use the File Open dialog. This dialog is opened by

•	choosing the Open command from the File menu,

•	pressing the key combination ("hotkey") Ctrl+O,

•	or by pushing the [image] button in the standard toolbar.

In the File Open dialog, you can change to other directories or (network) drives and even rename files or create new subdirectories. The File formats combo box can be used to select files with specific extensions only (e.g. "CIF").

Using the Recent File List

Previously opened files are stored in the "Recent File List". You will find a maximum number of eight file names at the bottom of the File menu to get faster access to previously opened files. In the Recent File List, you will also find files which have been saved previously with another name.

Using a file name as parameter or

Double-clicking a Diamond structure file

When you start Diamond, you can specify a file name to be opened as first structure document. Normally this method is used indirectly by the Windows Explorer when you double-click a DSF file. If Diamond is still running, a second window for that file will be opened.

Using Drag & Drop

You can drag a file from the Explorer or from the list of the Search Files to the desktop of Diamond desktop. This will then automatically open a window with the opened file.

Independent from the way you have opened the file, the format will be recognized automatically, and the file will be converted to a temporary Diamond file if needed.

For more informations, how far foreign file formats are supported, read the article "Importing Foreign File Formats".


Multiple Structure Descriptions in One File

Structure files may contain data for more than one (crystal) structure only. In this case, Diamond will open a special dialog window with a list, where you can select one (or more) structures from.

This example shows the Load dialog for a file which has been imported from the Inorganic Crystal Structure Database (ICSD), which contains 194 structure descriptions. Several brief informations are displayed in the list, such as the sequential number of the structure in the file (REL), the Hermann-Mauguin space group symbol and number, the formula sum, etc. The items in the list have been sorted for increasing space group number.

The Load dialog can also be opened later to load another structure from an open file. To do this, choose the Load command from the File menu, or press the "hotkey" Ctrl+L.

The list uses extended selection. To load one or more structures from the opened file, select the corresponding items, and then click the OK button.

Diamond opens a window for each structure that will get the title of the file with the zero-based sequential number of the structure. For example, when you open the third structure from a file "TEST.CRY", the new window will get the title "TEST-2.DSF".

Changing the settings of the Load dialog

The selection may be simplified if use a suitable sorting criterion. You can sort for a special kind of data by clicking on the header of the corresponding column. With a second and third click, you can invert the sorting criterion from increasing to decreasing or vice versa. These settings as well as the selection and arrangements of columns is done in the Structure list format dialog, which is opened from the Load dialog with the Settings button.

To add a new column to the list, select the item in the list "Not selected items", and push the ">>" button. To remove a column instead, select the item in the list "Selected items", and push the "<<" button. The sorting criterion can be changed from the combobox "Sort for" and the checkbox "Descending", or by clicking on the column header as stated above.

To change the width of a column, drag the separator between two columns to the left or right, rsp.

The selection of columns, their widths and the sorting criterion will be saved automatically in the Diamond configuration file, when you close the Load dialog.

Copying and printing the list

To copy the selected rows of the list to the MS Windows clipboard, push the Copy button. These can be pasted into other applications as text or table (word processor, spread sheet, database).

The complete list or the selected rows only can be printed, if you push the Print button. Diamond scales the printout automatically to the width of the page.


Searching Structure Files

Structure files in several directories or even your complete hard disk can be searched for selected data. These files may be Diamond Structure Files (DSF 2 format) or even foreign files that Diamond is capable of reading. In the latter case these foreign files will first be converted to temporary DSF 2 files and then searched.

To perform a search in selected files, choose the Search command from the File menu, or click the [image] button in the standard toolbar. This will show the Search Files dialog:

Choosing the directory/ies and file type(s)

The file search can be performed in one directory or in all sub-directories of a selected directory. Enter the search path in the Path input field.

The search path defined in Path as well as the setting Include sub-directories define what files will be searched. The setting Foreign formats, too defines the formats of the files to be searched. If neither Include sub-directories nor Foreign formats, too are active, Diamond only searches files in DSF 2 format that match one of the names defined in the search path. The names in the path can have the "wild cards" * and/or ?. Additionally disk drive letter and directory should precede. Example: "C:\PROGRAMS\DIAMOND2\ICSDDATA\AL*.DSF" searches all files in the directory "\PROGRAMS\DIAMOND2\DIAMOND\ICSDDATA" of drive C: beginning with "AL" and having the extension "DSF".

To browse through the directories or to select other (network) drives, choose the Browse button. In the Browse dialog, choose the directory where you want to start the search, enter the file name mask (e.g. "*.CIF" or "AL*.DSF") in the input field File name, and then press OK.

The setting Include sub-directories enables you to search entire directories trees - even complete disk drives. Example: "C:\*.DSF" searches all DSF files of drive C:.

If the setting Foreign formats, too is active, not only files in DSF 2 format are searched but also files in foreign (i.e. non-DSF) formats - as far as they are defined in the search path. The same file formats as in the file open procedure of Diamond are supported: CIF, SHELX, CSD-FDAT, PDB, Crystin, and XYZ. Foreign formats are recognized automatically. Diamond creates temporary DSF 2 files for that search.

Choosing the search criterion

To choose what Diamond shall find in the selected files, use the What to search for... button. This will open the What To Search For dialog:

The search criterion is divided into the following blocks:

Text	Performs a text search in fields of selected categories. The search can be case-sensitive and/or sensitive for complete words.
Chemical composition	Searches for the count and presence of specified elements and/or for structures with a specified formula type.
Space group	Searches for structures with selected space group(s).
Cell volume	Searches for structures with a cell volume within a given range.
Code(s)	Searches for the given reference code(s).
Date	Searches for structural descriptions created or last updated within a range of time.

Each block has a checkbox that enables or disables search for that category. For example, if only the Text checkbox is checked, Diamond will perform a text search only. It will not search for chemical composition, cell volume etc. in that case. If multiple blocks are activated (that means their checkboxes are checked), the results from the searches will be connected logically AND. For example, if you search for structures with the author name "Smith" and containing the elements Si, Al, and O and having a monoclinic space group, you must:

(1) activate the corresponding checkboxes (Text, Chemical composition, and Space group),

(2) activate the checkbox Author(s),

(3) enter the name "Smith" in the input field Text fragment,

(4) enter the elements "Al Si O" in the input field Element(s),

(5) check the radio button Number acc. to International Tables,

(6) enter the range of the space group numbers: 3 and 15, rsp.

Some hints for text search

If a text search has been selected, Diamond searches for the text specified in the Text (fragment) input field. It will search all text categories that are selected with the corresponding checkboxes, such as the authors' names, the title, several names, etc. For example, if both checkboxes for common and systematic name have been checked, and "chloride" has been entered in the text fragment field, all structures match with "chloride" either as common or systematic name. Select all text fields to be searched, if you do not know where the text (fragment) may be stored. (Please note: Diamond makes no text search in other fields, for example in space group symbols.)

If the checkbox as word is checked, a text fragment found is registered as match only, if it represents a whole word, but not if it is only part of a longer word. That means neither the last character before nor the first character after the matching fragment must be a letter.

If the checkbox case-sensitive is checked, the comparison is case-sensitive, that means "Structure" and "structure" would be treated as different.

Searching for chemical composition

There are three data fields for the search for chemical composition:

Element(s)	If you want to check the presence of several elements, specify their element symbols in this input field. (Use blanks to separate multiple element symbols.) If the checkbox OR connection is NOT checked, only structures match where all given elements occur. Otherwise all structures match with at least one of the mentioned elements.
Formula type (ANX)	If you want to check for compounds with a special stoichiometric composition, specify the formula type in this input field.
Element count	Defines the number of different chemical elements that a matching compound must have. A single value can be specified as well as a range of numbers (the lower number in the left, the higher in the right input field).

If you want to search for chemical composition, at least one element or a formula type or a value for the number of the elements must be specified! Multiple definitions are connected logically AND. That means, if you specify "Cs Ti O" as elements, "ABX3" as formula type, and 3 as element count, only structures will match with exactly the three elements Cs, Ti, and O and the composition CsTiO3.

Diamond will search the formula sum to evaluate the chemical composition of a structure, which has been generated from the atomic parameter list. The other formulas (used in Diamond as bibliographic data) will not be evaluated for that purpose.

Searching for space groups

You can either search for a specific Hermann-Mauguin space group symbol, or for a space group or a range of space groups. The latter are defined by the International Tables space group numbers (1 through 230).

Starting and stopping the search

Now back to the Search Files dialog. After search criterion and path have been defined or checked, the searching procedure can be started with the Start search button. The search is performed in a separate thread, that means, you can continue your work with Diamond, while the file search is running. (For that case, you can minimize the Search Files window.)

You may stop the searching thread, before it is ready, by clicking again on the same button (which has the text "Stop search" during the search process).

Opening matching files

The number of scanned files as well as the number of files with at least one matching structural description is displayed above the result list, where all matching files will be listed. To open one or more files from the list of matching files, select the files and push the Open button. Otherwise push the Done button. The settings of the Search Files dialog (but not the result itself) will be stored in the Diamond configuration file, including the search criteria.


Saving Structural Data

All data of the structure document (structural parameters as well as picture data) will normally be saved in a file with the Diamond Structure File format (DSF 2 format). Only this format stores all data to reproduce a structure picture exactly when it is opened later.

To save the structure document with the existing name (which is given in the structure window title)

•	choose the Save command from the File menu,

•	or use the "hotkey" Ctrl+S,

•	or push the [image] button in the standard toolbar.

To save the structure document with another name (or in another directory or on another drive), choose the Save as command from the File menu. This will open the Save As dialog. The existing name of the structure document is displayed in the File name input field. Do not change the setting in the File type combo box (which is "Diamond 2 (*.DSF)" whenever the Save As dialog is called), unless you want to export the structure in another format (see the article "Exporting Structural Data to Foreign Formats"). When the structure document is saved with a new name, this new name becomes the new title of the structure window.

Saving all structures

If multiple structure documents (in multiple structure windows) have been opened, you can easily save them all with the existing names by choosing the Save all command from the File menu.


Exporting Structural Data to Foreign Formats

To save structural data in a non-DSF format, choose the Save as command from the File menu. This will open the Save As dialog. Since the default file format is the DSF 2 format, you should first select the desired foreign file format.

Diamond offers two kinds of formats:

(1) Formats to save structural parameters.

(2) Formats to save graphical data.

The saving of graphical data (bitmap, metafile, or VRML file) is treated in the article "Saving the Structure Picture as Metafile, Bitmap, or VRML File".

Structural parameters can be saved in the following formats:

File format	Default extension	Description
Diamond 1.x	DS1	Binary file format used by Diamond version 1.x (compare the article "Compatibility with Diamond 1.x File Format").
CIF	CIF	Crystallographic Information File.
CRYSTIN	CRY	The download format which is created by the retrieval system of the Inorganic Crystal Structure Database (ICSD).
CSD-FDAT	CSD	The FDAT format which is created by the "SAVE 3" command from the retrieval system of the Cambridge Structural Database.
Protein Data Bank	PDB	The Brookhaven Protein Data Bank format.
SHELX	DAT	The Shelx-93 format.
XYZ	XYZ	The XYZ format.
Schakal	DAT	The Schakal format.


Auto Save Function

Diamond saves the structure documents of all structure windows in defined time intervals in temporary files. These files can be used to restore structure documents, which have been left due to a system crash or caused by an improper exit of Diamond. When a new session of Diamond is started after such a crash, these documents will automatically be restored to the condition when the structure document has been auto-saved the last time. The document cannot be restored, if the document has not been auto-saved because a new document was younger than the auto-save time interval.

To change the settings of the Auto Save function, choose the Options command from the Tools menu. From the Options dialog, choose the Desktop page. To enable the Auto Save function, check the Auto-Save checkbox. Enter the time interval (in minutes) in the Interval (min.) input field to change the auto-save interval.


Temporary Files

Diamond uses temporary files in the following cases:

(1) If the opened file has no DSF 2 format, the foreign format file is converted into a temporary file in DSF 2 format. This file is used to read the structural data directly, if the file contains one structure only, or to perform the Load dialog.

(2) If the file contains multiple structure descriptions, a temporary file is created for every single structure document that is loaded from the Load dialog.

(3) If the Auto Save function has been activated, the contents of all open structure documents will be saved in temporary files from time to time.

The temporary files will be deleted after the corresponding structure windows are closed. A temporary file that has been created from a foreign file containing multiple structure descriptions, will be deleted, when the last structure window is closed that works with data from that file.

Diamond stores temporary files in the "Temp" subdirectory of the Windows directory, or in the directory that is specified with the environment variable "TEMP=xxx" or "TMP=xxx".

If a Diamond session is closed irregularly, these temporary files will stay in the temporary files directory, and you can delete them later manually, for example from the Windows 95 or NT Explorer.

Never delete temporary Diamond files when Diamond is running!


Editing of Structural Data: Overview

This chapter describes:

•	how the parameters for a new structure are entered,

•	or how structural parameters are changed thereafter.

Bibliographic data can be entered or changed in the "Bibliographic data" dialog. These data do not influence the (crystal) structure and are thus not mandatory.

For the input or change of the structural parameters, Diamond offers three commands in the "Edit" menu:

•	Selecting the space group,

•	Editing the cell parameters,

•	and editing the atomic parameters including displacement parameters.


Editing Structural Data: New Structure Window

If you want to enter a new structure, that means you intend to enter all structural parameters manually, you must create a new structure window. This can be done either by:

•	Clicking on the [image] button in the standard toolbar,

•	choosing the command "File | New" from the main menu, or

•	using the Ctrl+N hotkey.

The structure in the new window is equipped with a minimum of necessary structure informations:

Space group: P1 (no. 1)

Cell parameters: a = b = c = 1 Å; alpha = beta = gamma = 90 degrees.

Atomic parameters: No atoms given.

You may change these data at any time.


Editing Structural Data: Bibliographic Data

Diamond treats bibliographic data as simple text. None of the bibliographic data is mandatory for the structure picture. They are used to store additional data about a crystal structure publication or comments from the author. Bibliographic data appear in the data sheet as well as in text strings in the structure picture.

To edit bibliographic data, choose the Bibliographic data command from the Edit menu.

Diamond uses the following data fields:

•	Structural formula,

•	analytical formula,

•	trivial (common) name,

•	systematic (IUPAC) name,

•	structure type,

•	mineral name,

•	source of compound or origin of the mineral,

•	measured formula weight,

•	measured density,

•	melting point,

•	resdiual factors Rall and Robs,

•	number of formula units per cell (Z),

•	title of publication or some other assigned title,

•	name(s) of the author(s),

•	ASTM Journal Coden, publication year, volume, first and last page,

•	Chemical Abstracts code,

•	origin (crystallographic database),

•	database-specific reference code,

•	recording date and latest update (database),

•	creation method,

•	database-specific remarks,

•	comments.

Superscripts and subscripts in the title or in the name fields are coded by enclosing carets (^ - for superscripts) and tildes (˜ - for subscripts) analogous to the CIF conventions. Therefore the string H˜2˜O appears as H2O in the data sheet whereas Fe^2+^ appears as Fe2+.

Do not use special characters when coding the formulas, because digits are automatically interpreted as indices. Try to reproduce the compound structure in the formula by using suitable parentheses.


Editing Structural Data: Space Group

The symmetry of the compound is defined by the space group. The space group is defined by the Hermann-Mauguin symbol plus an internal number to distinguish different settings of a space group. This number should not be mixed with the space group number defined in the International Tables for Crystallography, which has a range from 1 through 230.

A valid space group symbol is mandatory for Diamond. Otherwise symmetry-induced atom positions cannot be calculated and therefore a crystal structure cannot be displayed correctly.

To edit the space group, choose the Symmetry command from the Edit menu.

Diamond uses a space group information file that contains comprehensive informations for a total number of 670 space group settings. 530 of these space group settings are defined in Volume A (Space-Group Symmetry) of the International Tables for Crystallography. These 530 settings contain 230 standard settings plus additional settings for several monoclinic cell choices, unique axes, origin choices, or rhombohedral settings. Another set of 140 settings have been taken from the Inorganic Crystal Structure Database (ICSD), which are in parts identical with the 530 other settings but have special symbols to indicate e.g. the origin choice (e.g. "Fd3-mS", which corresponds to origin choice 1 in IT and is not centrosymmetric, whereas "Fd3-mZ" corresponds to origin choice 2 and is centrosymmetric).

Diamond offers a versatile dialog to select the right one out of the 670 space group settings. The 230 standard space groups are listed in a so-called tree view control. Additional settings are available by opening the corresponding node.

The example shows settings for space group no. 14. P 1 21/c 1 is the "standard" setting, whereas P 1 21/a 1 is highlighted. This setting has unique axis b and cell choice 3 like stated in the info field.

The Diamond space group info file contains the following informations for most of the space group settings. (Some informations such as special positions, Schoenflies symbol are not mentioned for the 140 space group settings from ICSD.)

Internal Space Group Number	The space group number which is handled internally by Diamond to distinguish between different settings of a space group. The first setting according to International Tables of Crystallography (IT) is: IT number * 100 (e.g. 1400 for P 1 21/c 1). Further settings are numbered with IT number*100+1, +2 etc. (e.g. 1401 for P 1 21/n 1; 1402 for P 1 21/a 1 etc.). Special settings from ICSD are numbered 2400, 2500 etc.
Int. Tables or Equivalent No.	The space group number according to IT, this has a range of 1 through 230.
Hermann-Mauguin Symbol	The full form of the Hermann-Mauguin symbol from IT or the ICSD notation (e.g. P121/C1S)
Hall Symbol	The Hall space group symbol according to: Hall, S. R. (1981). Acta Cryst. A37, 517-525.
Schoenflies Symbol	The Schoenflies symbol from IT
Point Group	The short symbol for the point group which the space group belongs to
Laue Group	The symbol of the Laue class
Crystal System	The crystal system
Centrosymmetric	Indicates the presence or absence of centrosymmetry
Centering	The centering
Monoclinic axis	The unique axis if the crystal system is monoclinic
Monoclinic Cell Choice	The number of cell choice in IT
Monoclinic Setting	The monoclinic setting, e.g. "c-ba" for A 1 2/a 1 (no. 15)
Symmetry Matrices	The coordinate triplets of the symmetry matrices of the space group including sequential number
Positions	The positions with multiplicity and Wyckoff letter of the sites, beginning with the general site, and the coordinate triplet of the first symmetry matrix of the general/special site.

This is an example for space group P 1 21/c 1 (no. 14):

Internal Space Group Number:	1400
Int.Tables or Equivalent No.:	14
Hermann-Mauguin Symbol:	P 1 21/c 1
Hall Symbol:	-P_2ybc
Schoenflies Symbol:	C2h^5
Point Group:	2/m
Laue Group:	2/m
Crystal System:	Monoclinic
Centrosymmetric:	yes
Centering:	Primitive (P)
Monoclinic axis:	b
Monoclinic Cell Choice:	1
Monoclinic Setting:	abc
Symmetry Matrices:
(1)	x, y, z
(2)	-x, 0.5+y, 0.5-z
(3)	-x, -y, -z
(4)	x, 0.5-y, 0.5+z
Positions:
4e	x, y, z
2d	0.5, 0, 0.5
2c	0, 0, 0.5
2b	0.5, 0, 0
2a	0, 0, 0

"Only" the following informations about a space group setting are important for Diamond:

(1) The internal space group number.

(2) The symmetry matrices of the general position in the right order (the sequence number of the symmetry matrix is used in the atom code).

(3) The Bravais translations according to centering, e.g. "+1/2,1/2,1/2" for I-centering.

(4) The symmetry matrices of the special position - together with multiplicities and Wyckoff letters - are used to calculate the correct Wyckoff positions in the atomic parameter list.

Other informations such as centrosymmetry, monoclinic cell choice etc. will not be used for the creation of atoms, but are helpful for the decision of the right setting.


Editing Structural Data: Cell Parameters

The six cell parameters a, b, c, alpha, beta, and gamma define the dimensions of the unit cell. a, b, and c are the lengths of the unit cell base vectors, whereas alpha is the angle between the vectors b and c, beta the angle between a and c, and gamma the angle between a and b. a, b, and c must be given in Angstroem, the angles in degrees.

For a usual crystal structure, which has translational symmetry, the cell parameters are mandatory, since they are necessary to calculate "real" coordinates from the fractional coordinates of the atomic parameter list, and thus to calculate distances and angles, thermal ellipsoids etc. correctly.

To enter or change the cell parameters, choose the Cell command from the Edit menu.

The cell parameters must fit with the crystal system of the actual (or previously set) space group. That will be no problem, if you begin with a new structure, since space group P1 is preset. But in most cases another space group has been defined, which may have restrictions to the cell parameters. The Cell parameters dialog has a special setting which disables all non-mandatory cell parameters. For example, b, c, alpha, beta, and gamma cannot be changed, if a cubic space group has been set.


Editing Structural Data: Atomic Parameters

The list of atomic parameters contains the positional as well as chemical informations about all atoms of the (crystal) structure. For the regular case, that means, the compound is a crystal structure with translational symmetry, the atoms in the parameter list describe only a set of atoms which is reproducible for the entire lattice by symmetry operations and cell translations. In that case this set of atoms is often called the "asymmetric unit".

Each atom in the "real world" of the crystal structure can thus be reproduced from an atom of the asymmetric unit by defining a code describing the symmetry operations to produce this atom. The coordinates of the atoms of the asymmetric unit refer to the base vectors of the unit cell and are thus fractional (x/a, y/b, z/c) and ideally (but not necessarily) in the range 0 <= {x,y,z} < 1.

To add atoms to the parameter list, delete atoms, or to change parameters, choose the Atomic parameters command from the Edit menu.

Diamond has no restrictions for the total number of atoms in the parameter list.

Parameters of each atom

For each atom, the following parameters can be defined:

Element	The element symbol (and thus the ordinal number) of the atom. Deuterium (D) and tritium (T) are treated as separate elements. If no (valid) element symbol is given, a dummy atom will be assumed (see below).
Symbol	The symbol that briefly describes the atom on this site, usually (but not mandatory) the element symbol plus an index of letter, e.g. "Fe 1", or "C1A".
Oxidation number	The oxidation number or charge of the atom
Site occupation factor	The fraction of the atom statistically present at this site, usually a value between 0 and 1.
Number of attached H atoms	The number of hydrogen atoms attached to the atom at this site, for which no coordinates (measured or calculated) have been determined.
Position	The Wyckoff position, consisting of multiplicity and Wyckoff symbol (letter) of the general or special site rsp. An asterisk (*) or question mark (?) may be given for the letter if only the multiplicity is given.
x, y, z	The fractional coordinates of the site. Standard uncertainties may be given. Coordinates on special sites may be given as fractions.
Site	A standard code to signal if the site has been determined by diffraction data or calculated from the geometry of surrounding sites, or has been assigend dummy coordinates.
Description	A description of special aspects of this site.
Type of displacement parameter(s)	Describes if an isotropic or equivalent or anisotropic or no displacement parameters are available for this site, and eventually the type of displacement parameter(s). See below.
Isotropic or equivalent displacement parameter	The isotropic atomic displacement parameter or the equivalent atomic displacement parameter calculated from anisotropic atomic displacement parameters. See below.
Anisotropic parameters	The standard anisotropic atomic displacement parameters. See below.

Mandatory parameters

The following parameters of an atom are mandatory:

(a) If the atom site has valid coordinates (determined by diffraction or calculated), x, y, and z are mandatory. If the site is no dummy site (see below), a valid element symbol must also be given. Oxidation number, site occupation factor, number of attached hydrogens are not necessary to be given. The Wyckoff symbol will be calculated automatically by Diamond when the Atomic parameters dialog is closed with OK.

(b) If the position of the atom has not been determined, the coordinates x, y, and z are undefined. In most cases this "atom" describes H atoms which have not been localized in the unit cell. In such cases the site occupation may exceed 1. If e.g. the site occupation is 5 and the multiplicity is 4, there are 5 * 4 = 20 atoms in the unit cell with no positional parameters.

Dummy atoms

The element of the atom site (and thus the ordinal number) is defined by the element symbol, including 'D' and 'T' for deuterium and tritium, rsp. A dummy atom, i.e. an atom with well-defined site but without chemical meaning, may be defined by entering a '*' as element symbol (or leaving it blank). Dummy atoms represent a special kind of atom type. A dummy atom is useful to define coordination polyhedra with no central atom.

Mixed sites

If a compound contains mixed sites, you must specify an atom for each part of the site. Example: The site with coordinates (0; 1/2; 0.2345) is occupied 25 percent by Si and 75 percent by Al. In this case two atoms must be defined in the parameter list: Si with a site occupation factor of 0.25 and Al with a site occupation factor of 0.75. For more information, see the article "How mixed sites are determined and treated...".

Formula sum, calculated formula mass and density

Diamond uses the atoms in the parameter list also to determine the formula sum, the formula mass and the density.

Changing position in parameter list

The order of the atoms in the parameter list can be changed by dragging the actually marked atom to the desired position.

Changes in the structure picture

If a structure picture has already been defined, changes in the atomic parameter list can have different effects on the picture, since all created atoms base upon the atoms of the parameter list:

Adding an atom to the parameter list:

This has no effect on the picture, since Diamond never creates automatically atoms from the parameter list.

Deleting an atom from the parameter list:

All created atoms basing upon the deleted atoms will be destroyed.

The position of an atom has been changed:

The coordinates of all atoms basing upon the changed atom will be recalculated. This may result in "strange distortions". Please note that bonds will not be affected. That means, no bonds will be destroyed, if the bonds get "too long" or "too short". Positions do not split if the multiplicity of an atom site increases, e.g. from a special to the general site. On the other hand, two or more atoms may share one and the same position, if the multiplicity decreases, e.g. from the general site to a special site.

The element has changed:

The elements of all corresponding created atoms change. But the designs must be update manually according to the new atom type of the created atom.

Note that on any changes in the atomic parameter list the lists of atom types and bond types will be rebuilt and thus connectivity will be reset!


Building Up Structural Parts: Overview

This larger section of the Diamond online user manual describes the broad variety of functions that build up structural parts or help to destroy these parts.

After structural data has been imported - mostly from a foreign format structure file - or entered manually, you first have to build up an appropriate part of the structure, before you can see any graphical representation.

The first chapter will make you familiar with the differences between several kinds of atoms, especially the atoms in the parameter list and the atoms in the structure picture, as well as bonds. See "About Atoms, Atom Types, Bonds, and Bond Types: Overview".

Before the several building up functions are described, the universal filter function is presented, which can be useful to exclude particular elements from the generation procedure. See "Filter: Overview".

The first chapter about building up structures, handles the probably easiest way to get an overview of the crystal structure, especially for crystal structures without molecular subunits or structures where molecules do not play a major role: That is the generation of atoms within a range of the lattice. This range may have the shape of a (rectangular) parallelepiped or of a sphere. See "Filling Cell Ranges: Overview".

The following chapters describe how atoms in (coordination) spheres around all or selected atoms can be generated, and how atoms can be connected with bonds. See "Spheres: Overview" and "Generating Bonds: Overview", rsp.

Another strategy starts from a single, free selectable atom. This atom serves as some kind of focal point, and the structure can be build up sphere by sphere around this atom. This method is especially designed to become acquainted with a previously unknown structure. "Generating Atoms Directly: Overview" will describe how single atoms can be generated by applying suitable symmetry operations to atoms of the parameter list.

If molecular substructures can be localized, Diamond is able to recognize molecules and molecule ions without any explicitely given connectivity, and display them as isolated units, even if they do not fit into the borders of the unit cell or another given cell range. See "Molecules: Overview".

Of course, the mentioned strategies may be combined. For example, you may first fill up a cell range, and then complete all molecular fragments selectively to get a so-called packing diagram.

With Diamond, any interesting structural property can be preparated in a suitable way.


About Atoms, Atom Types, Bonds, and Bond Types: Overview

In the usual case, that the compound is a crystal structure with translational symmetry, each atom of the structure picture (e.g. the molecule or the contents of the unit cell) bases upon an atom in the parameter list. The atom in the picture, here called the "created atom", is constructured by applying suitable symmetry operations and (integer) cell translations. Both index of the atom in the parameter list and symmetry operations are coded in the atom code.

Additionally, the atoms of the parameter list are grouped together in a list of so-called "atom types". By default, atom types differ by ordinal number and oxidation number. Diamond groups all atoms having the same ordinal number and oxidation number into one atom type. These atom types have a lot of properties (radii, design etc.) which serve as basis for the corresponding properties of the created atoms.

The list of bond types contains all N * (N + 1) / 2 combinations of N atom types. These bond types contain the bonding spheres for those building functions that create bonds, e.g. the generation of molecules. The definitions of bonding spheres is collected in the connectivity list. Furthermore, bond types contain the basic properties for the designs and radii of the bonds in the structure picture, here called the "created bonds".

For details about atom types, bond types, created atoms and bonds, read the following articles:

Definitions

Mixed Sites

Atom Types

Atom Codes

Assigning a New Atom Type at Runtime

Bond Types

Connectivity

Created Atoms

Created Bonds


About Atoms, Atom Types, Bonds, and Bond Types: Definitions

The following definitions about the different kinds of atoms and bonds used in Diamond refer to the usual case that the compound is a crystal structure with translational symmetry. That means the compound is built up by a three-dimensional lattice with an infinitesimal number of equal copies of the unit cell.

Created atoms

In Diamond, the atoms in a structure picture are called "created atoms", since Diamond does not automatically create atoms from the atoms in the parameter list. (The following chapters will tell you a lot of functions to create atoms, such as filling a cell range or creating molecules.). Each of these created atoms has been produced from an atom of the parameter list by applying suitable symmetry operations and - as far as necessary - cell translations.

Atom codes

The atom code is the identifier for both the index of the atom in the parameter list and the symmetry operations and cell translations to be applied to produce the "created atom". See Atom Codes for a detailed definition and examples.

Atom types

The list of atom types is a collection of atoms from the parameter list, which differ only in ordinal number and oxidation number. Mixed sites are treated in a rather complicated way. For details and examples, see Mixed Sites and Atom Types. Atom types are used to group atoms with common chemical properties together and to define the basic design for the created atoms.

Bond types

Bond types are created from the atom type list. Each bond type represents one atom type combination. That means, for N atom types, we get N * (N + 1) / 2 bond types. Like atom types, bond types define the basic design for "created bonds".

Created bonds

Whereas each created atom can be reduced to a definite atom of the parameter list, bonds cannot. (Diamond has no equivalent to an atomic parameter list.) A bond is created by one of the bond creating functions of Diamond, but only if the atom type combination (the bond type) is (a) enabled for bonding and (b) if the interatomic distance is within the bonding sphere.

Connectivity

The connectivity list is derived from the bond type list. Thus it contains all N(N+1)/2 combinations of N atom types of a structure. For each atom type pair a bonding sphere is defined and a flag if this bonding sphere is active or not, i.e. whether bonds are allowed for that atom type pair or not. Diamond offers a sophisticated method to edit and check the connectivity. For details, see Connectivity.


About Atoms, Atom Types, Bonds, and Bond Types: Mixed Sites

Whenever atoms are created from atoms of the parameter list, Diamond does not access the parameter list directly, but makes use of a separate list, which contains all sites of the unit cell. If the structure does not have any mixed sites, that means two or more atoms do not share the same position, the list of sites has as many entries as the sum of the multiplicities of all atoms of the parameter list with valid coordinates.

This has the advantage that Diamond needs not apply symmetry operations and Bravais translations for each atom to be created but only the integer cell translations as far as necessary.

Another important reason for Diamond to work with the site list is to prevent the creation of multiple atoms on one and the same position. This would happen, if all symmetry operations would be applied to an atom on a special site.

If the structure has mixed sites, Diamond processes only one representative for all atoms sharing the same site. The representative of a site is the atom with the highest site occupation factor. If some or all atoms on the site have the same site occupation factor, the first one of these atoms in the parameter list will be taken. The non-representative atoms on this site will become "buddies" of the representative. These buddies are often trace elements.

The site list is invisible for you, but you have several functions to get informations about the number of sites as well as mixed sites:

(1) The total number of sites (the sum of multiplicities) is part of the Pearson symbol in the data sheet and additionally given on the Contents page of the Properties dialog, which you can open with the Properties command in the File menu.

(2) The composition of mixed sites can be visualized using alternative color differentiations, which you will find in the Color differentiation dialog, which is opened with the Color differentiation command in the Display menu.


About Atoms, Atom Types, Bonds, and Bond Types: Mixed Sites
About Atoms, Atom Types, Bonds, and Bond Types: Atom Types

The list of atom types is a collection of atoms from the parameter list, which differ only in ordinal number and oxidation number. The usage of a list of atom types separate from the list of atomic parameters has two main reasons:

(1) In most crystal structures, especially in "organic" molecular structures, atoms of the same species disperse on different sites. These atoms usually have the same or similar chemical properties and often similar coordination. Therefore, Diamond has many functions for building up or designing structural parts, which access the list of atom types instead of the list of atomic parameters.

(2) Each atom type defines the basic design for all created atoms basing upon an atom of the parameter list, that belongs to this atom type. Example: The atomic parameter list has three atoms of the species C (carbon) ("C 1", "C 2", and "C 3"). If the color for the atom type "C" is grey, all atoms which have been created from one of the atoms "C 1", "C 2", and "C 3" have also the color grey. (Colors of created atoms may be changed individually thereafter.)

Furthermore, an effective radius is defined for each atom type. This effective radius is the effective ionic or atomic radius used to define the bonding sphere, if no mean bond length value is available for a given atom type combination. See the articles about bond types and connectivity to get more informations how bonding spheres are calculated.

Different atoms sharing the same site (mixed sites) are grouped together in separate atom types. If e.g. a structure has both Si and Al on single sites and additionally one site with 50 percent Si and 50 percent Al, this will result in at least three atom types: 1. Si; 2. Al; 3. SiAl. If there are more mixed sites with Si and Al, this will result in the same atom type "SiAl", even if the composition varies (e.g. 25 percent Si and 75 percent Al instead of 50 : 50).

Ordinal number, oxidation number - as far as defined -, and eventually mixed sites are the criteria for Diamond to differentiate the atoms in the parameter list, when the list of atom types is initialized. This happens whenever a structure has been imported or the atomic parameter list has been edited. Beyond that, you can change the default assignment of atom types to atoms of the parameter list. The article "Assigning a New Atom Type at Runtime" explains how this is done.


Assigning a New Atom Type at Runtime
About Atoms, Atom Types, Bonds, and Bond Types:
Assigning a New Atom Type at Runtime

Whenever a structure has been imported or the atomic parameter list has been edited, Diamond initializes the atom type list automatically. All atoms with the same ordinal number (or ordinal numbers if it is a mixed site) and - as far as defined - the same oxidation number, are grouped together to one atom type.

If one ore more atoms belonging to the same atom type, but have different chemical properties or different coordinations, you can assign it or them a new atom type, using the following steps:

1. From the Edit menu, choose the Atom types command.

2. On the Definition page of the Atom types dialog, select the atom type, where the new atom type is to be derived from.

3. Push the New button. (This inserts a copy of the original atom type into the atom type list; the symbol of the copy has an "A" attached to the original symbol; you may edit the symbol if needed.)

4. Push the Assign to button. (This opens the Assign atom type dialog.)

5. From the parameter list, select the atom(s), you want the new atom type to be assigned to, and then push the Assign button.

6. Close the Assign atom type dialog with "OK", when you have finished the assignments.

7. Close the Atom types dialog with "OK", when you have finished editing atom types and atom type assignments.

The new atom type will thereafter appear in the atom type lists used by several building and designing functions. So you can define coordination spheres for the new atom type, which are different from the "original" atom type, different designs, different coordination polyhedra etc.


About Atom Codes
About Atoms, Atom Types, Bonds, and Bond Types: Atom Codes

In the usual case, that means the crystal structure has translational symmetry, all atoms of the structure picture, here called the "created atoms", base upon atoms of the parameter list. A special code is stored with each created atom, which encodes the symmetry operations, Bravais translations and integer cell translations, which have been applied to produce this atom from the corresponding "asymmetric" atom in the parameter list.

The atom code consists of:

(1) the sequence number of the atom in the parameter list;

(2) the sequence number of the symmetry operation;

(3) the sequence number of the Bravais translation;

(4) three integer cell translations along the base vectors a, b, c of the unit cell.

The sequence number of the atom in the parameter list has a maximum value of 2^31 - 1. The sequence number of the symmetry operation has a maximum value of 48, that for the Bravais translation a maximum value of 4. Each integer cell translation has an internal range capacity from -128 through +127.

The sequential number of the symmetry operation refers to the sequential order of the symmetry matrices for the current space group, which are defined in the Diamond space group file. See the article "Editing of Structural Data: Space Group" how to get informations about the current space group. The symmetry operation with the number 1 is "x,y,z" in any case.

To get informations about the Bravais translations, choose the Filter dialog from the Edit menu. In the Filter dialog, view the list Bravais translations. The Bravais translation with the number 1 is "+(0,0,0)" in any case.

On input or output, the atom code has the form

AXYZSSB

with:

A	the sequential number of the atom in the parameter list, beginning with 1.
X	the integer cell translation along the a-axis of the unit cell, plus 5. E.g. a value of 6 means +1 into the a-direction, 3 means -2 into the a-direction.
Y	dito for the b-axis.
Z	dito for the c-axis.
SS	the sequential number of the symmetry operation, beginning with 1 ("01").
B	the sequential number of the Bravais translation, beginning with 1.

Since only one digit is reserved for each integer cell translation, "only" a range of -5 ("0") through +4 ("9") can be used for the integer cell translations on input. On output, an asterisk (*) marks an overflow.

Most of the building operations of Diamond do not face you with atom codes. But if you want to define atoms by code, see the article "Adding Some Atoms From the Parameter List" how to do this.


About Bond Types
About Atoms, Atom Types, Bonds, and Bond Types: Bond Types

A bond type is defined by a definite pair of atom types. The list of bond types is directly created from the list of atom types. For N atom types, we get N * (N + 1) / 2 bond types.

The usage of bond types has two main reasons:

(1) Each bond type defines the basic design for all bonds of the structure picture, here called "created bonds". Example: If the color for the bond type "P+5 - O-2" is yellow, all bonds between atoms belonging to atom types "P+5" and "O-2" have the same color yellow. (Colors of created bonds may be changed individually thereafter.)

(2) Each bond type has a definition, whether bonding is enabled for this atom type combination, and the dimension of the bonding sphere.

To edit bond types, choose the Bond types command from the Edit menu.

Since the discussion of bonding spheres is essential for the building functions of Diamond that create bonds, especially the generation of molecules, this is handled separately with the connectivity list.

To edit the connectivity list, choose the Connectivity command from the Structure menu. See the article "Connectivity" to get more information about the connectivity list.


About Connectivity
About Atoms, Atom Types, Bonds, and Bond Types: Connectivity

Since the definition of the bonding spheres in the bond type list is essential for all building functions that generate bonds, Diamond offers a separate and sophisticated way to handle these bonding spheres.

For each atom type pair (that means for each bond type) a bonding sphere is defined and a flag whether this bonding sphere is active or not, i.e. whether bonds are allowed for that atom type pair or not.

To edit the connectivity list, choose the Connectivity command from the Structure menu.

In the Connectivity dialog, you will find a list of all atom type combinations (bond types). Those atom type combinations which have been defined as bonded are listed in the combobox Bonding sphere. Additionally you will find the lower and upper value for the actually selected bonding sphere as well as the distribution of interatomic distances in the current structure.

Default initialization of connectivity list

Whenever a structure has been imported or the atomic parameter list has been edited, bond types will be initialized or reset, rsp. The bonding sphere of a bond type is calculated like this:

If a mean bond value is defined for the element combination of the bond type (ignoring oxidation numbers) in the Diamond configuration file, this value is taken as mean value of the bonding sphere. Otherwise, the effective radii of the two atom types are added.

The result is multiplied with the lower sphere boundary factor to get the lower boundary value of the bonding sphere. The upper sphere boundary factor is used for the upper boundary value. Diamond works with default boundary factors of 0.6 and 1.2 rsp.

To edit the boundary factors, push the Settings button in the Connectivity dialog, and edit the values in the Settings for connectivity dialog.

All bond type are selected, unless the oxidation numbers have the same sign.

Enabling or disabling bonding for an atom type combination

In the list Select atom pair(s) to be connected, click on the atom type you want to enable or disable rsp. Since the list works with multiple selection, each click on an item switches between "selected" and "not selected".

Changing the bonding sphere for an atom type pair

If the atom type pair has been selected in the list Select atom pair(s) to be connected, select the atom type pair from the combo box Bonding sphere. Then edit the lower and/or upper value in DMin and DMax rsp. or shift the red lines in the histogram.

To shift one of the red lines, move the mouse cursor to the line. (The mouse cursor changes its symbol.) Press the left mouse button and move the line to the desired position. When you have reached the final position, release the left mouse button. The new lower or upper value will be reflected in the DMin or DMax field as well as in the list Select atom pair(s) to be connected.

Please note that the calculation of the interatomic distances to be displayed in the histogram may take a while, especially for structures with some thousands of atoms in the parameter list (e.g. proteins).

Evaluating all bonding spheres

Click the Evaluate button. This will execute the following steps:

(1) All bonding spheres are reset to the initial values (see above: Default initializiation of connectivity list).

(2) For each bonding sphere, interatomic distances are calculated. A bond type will then be selected, if at least one distance is found within the bonding sphere range.

Resetting all bonding spheres

Click the Reset button. This will re-initialize the bonding spheres. (See above: Default initializiation of connectivity list.)


About Created Atoms
About Atoms, Atom Types, Bonds, and Bond Types: Created Atoms

In Diamond, the atoms in a structure picture are called "created atoms", since Diamond does not automatically create atoms from the atoms in the parameter list. (The following chapters will tell you a lot of functions to create atoms, such as filling a cell range or creating molecules.). Each of these created atoms has been produced from an atom of the parameter list by applying suitable symmetry operations and - as far as necessary - cell translations.

In principal, Diamond offers two adverse strategies how to generate atoms:

1. Selecting one, more, or all atoms from the parameter list, and applying symmetry operations and cell translations as far as needed.

2. Defining a range of the lattice, where atoms are to be generated and molecules are to be built, rsp.

The latter case is of course the much more important strategy for you, because the composition of the atoms in the parameter list (especially their coordinates) is difficult to handle, since in most cases the parameter list does not describe simply one molecule. When generating the atoms from the parameter list, Diamond automatically selects the right symmetry operations and cell translations. You normally do not have to worry about coordinates and atom codes.


About Created Bonds
About Atoms, Atom Types, Bonds, and Bond Types: Created Bonds

The current version of Diamond does not support direct bonding information in the structural input parameters. That means, since there is not equivalent to the atomic parameter list, whereas each created atom can be reduced to a definite atom of the parameter list, bonds cannot.

Instead, a bond is created by one of the bond creating functions of Diamond, but only if the atom type combination (the bond type) is (a) enabled for bonding and (b) if the interatomic distance is within the bonding sphere. Bonds will be created automatically when

(1) the surrounding atoms in the coordination spheres of selected (central) atoms are generated; (There is a similar function that fills spheres with fixed dimensions and that does not connect the surrounding atoms with the central atom.)

(2) molecules are built or molecular fragments are completed.

Furthermore, bonds can be generated at any time after atoms have been generated, e.g. after the generation of all atoms of the unit cell (a procedure which does not automatically create bonds). For details, see the article "Connecting All or Selected Atoms".

Bonds between two atoms, which do not belong to an atom type combination (that means to a bond type) that is enabled to be connected, or which are "too short" or "too long", can be created manually. See the article "Inserting a Bond Between Two Atoms".


Filter: Overview

Diamond offers a special function that can exclude selected atoms of the parameter list, selected symmetry matrices, or selected Bravais translations from being used during all functions that build up structural parts. By default this filter is not active, which means that all atoms, symmetry matrices, and Bravais translations will be considered.

Depending on your intention, it might be useful to exclude particular elements from the generation procedure. This can be done with the Filter dialog. See "Excluding Atoms or Symmetry Operations" how to do this.

This filter takes effect on almost every function that builds up a structural part. See "Effects of the Filter" how these functions are affected.


Filter: Excluding Atoms or Symmetry Operations

The exclusion of atoms, symmetry operations, or Bravais translations is managed with the Filter dialog.

To open the Filter dialog, choose the Filter command from the Structure menu.

Alternatively you can use the [image] button in the Build toolbar.

In the list Atom types you find all atom types of the current compound. In the list Atoms from parameter list all atoms from the atomic parameter list are mentioned separately. Therefore some atom types may be mentioned more than once. If you select an atom type, all corresponding atoms are selected automatically. To select all atoms belonging to an atom type except those of one particular site, first select the atom type, and then reset the selection of the desired atom site.

Each atom of the parameter list represents a particular number of symmetry equivalent atoms. These atoms arise from the application of the symmetry operators and Bravais translations, which are defined by the space group. Symmetry operators and Bravais translations of the current structure can be found in the corresponding lists Symmetry operations and Bravais translations.

By choosing only one single atom, one symmetry operation, and one Bravais translation, only one atom can be generated. But note that you have to select at least one atom, operator, and translation, because otherwise no atoms can be generated.

The selection of atoms has an effect on all following operations, which generate atoms. If the status of the current selection is overlooked, this can lead to misunderstandings. Therefore DIAMOND shows a warning symbol at the lower left corner of the structure window, whenever an atom or operator is excluded:

This is no error message, but it should remember you, that some atoms could not be generated, though you might expect this.

To reset the exclusion of atoms, symmetry operations, or Bravais translations (that means to switch off the filter), use the Select all button in the Filter dialog, and then press OK.

An easier way to switch off the filter, is to click on the [image] button in the Build toolbar.

The warning symbol [image] will disappear after the filter has been switched off.


Effects of the Filter

The exclusion of atoms, symmetry operations, and Bravais translations takes effect on the following building operations:

1. Generation of atoms within distinct ranges of the crystal structure lattice (unit cell, enclosure boxes around a selected atom, etc.). See "Filling Cell Ranges: Overview".

2. Filling of fixed spheres as well as of coordination spheres. See "Spheres: Overview".

3. Generation of molecules and completion of molecular fragments. See "Molecules: Overview".

The filter also takes effect on the construction of coordination polyhedra, since atoms within the coordination spheres may be generated if necessary. See "Coordination Polyhedra: Overview".

The filter does not take effect on the direct generation of atoms using the Add atoms command or the Add all atoms command from the Structure menu. See "Generating Atoms Directly: Overview".


Filling Cell Ranges: Overview

For crystal structures without molecular subunits or structures where molecules do not play a major role, the probable easiest way to get an overview of the crystal structure is to generate atoms within a range of the lattice. This range may have the shape of a (rectangular) parallelepiped or of a sphere. Here in Diamond, we calls this generation of atoms within a given range, shortly "Filling", e.g. filling the unit cell.

Unit cell

The most common way of filling a range of the lattice is to fill the unit cell. See the article "Filling the Unit Cell" how to do this.

Super cell

If a crystal structure has a rather small unit cell, filling of a super cell affords a more impressive overview of the structure. A super cell is an integer multiple of the unit cell. See the article "Filling a Super Cell" for details.

Cell range

An arbitrary range of the lattice can be filled by defining six distinct values as border values of a parallelepiped. These borders can refer to the crystal coordinate system as well to "real world" coordinate systems like the reference or view coordinate system. See the article "Filling a Cell Range" for details.

Filling a box or sphere around a central atom

Another way to define a parallelepiped to be filled, is to choose an atom from the parameter list as center and to specify the radii of the parallelepiped, which is then often called "(enclosure) box". This can also be defined for a sphere instead of a parallelepiped ("enclosure sphere"). See the article "Filling Boxes or Spheres Around Selected Atoms" how this is done.

Filling a Rectangular Area of the Screen

A special, interactive version of filling a rectangular parallelepiped with borders parallel to the current viewing box, is to define a rectangular region on the screen (in the structure window) and to define the depth of the box numerically. The article "Filling a Rectangular Area of the Screen" describes how this can be done.


Filling the Unit Cell

Filling the unit cell means the generation of all atoms with crystal coordinates with -epsilon <= X <= 1 + epsilon and  -epsilon <= Y <= 1 + epsilon and -epsilon <= Z <= 1 + epsilon.

The epsilon value prevents atoms which are (nearly exactly) on edges or faces of the unit cell from being excluded during the filling procedure. If epsilon is e.g. 0.01, the real cell range to be filled has XMIN=YMIN=ZMIN= -0,01 and XMAX=YMAX=ZMAX= 1,01 in crystal coordinates.

To fill the unit cell, choose the Unit cell command from the Fill submenu of the Structure menu.

Alternatively, you can use the button [image] from the Build toolbar or the acceleration key Shift+Ctrl+U.

The filling of the unit cell is affected by the filter, which is described in details in the article "Filter: Overview".

By default, this function also generates the edges of the unit cell automatically. If you do not want cell edges to be created automatically when filling the unit cell, do the following steps:

1.	From the Structure menu, open the Fill submenu and choose the Super cell command.

2.	In the Fill super cell dialog, switch off the checkbox Generate cell edges automatically.

3.	Choose the option Unit cell from Select super cell.

4.	Close the dialog with OK.

Diamond will save the setting Generate cell edges automatically in its configuration file. That means, in all subsequent calls to a function that fills the unit cell or a super cell, no cell edges will be created automatically. To re-enable the automatic generation of cell edges, repeat the above step, but switch on the Generate cell edges automatically checkbox.

Use the Fill super cell dialog, too, if you want to change the epsilon value.

See also:

Filling a Super Cell


Filling a Super Cell

The usage of a so-called "super cell" instead of the unit cell only, is an alternative way to get insight into a bigger part of the crystal structure, especially if the unit cell dimensions are rather small. A super cell is defined as an integer multiple of the unit cell.

To fill the contents of a super cell, choose the Super cell command from the Fill submenu of the Structure menu. This opens the Fill super cell dialog.

The following types of super cells (including the rather simple unit cell itself) are available. (XMIN, YMIN, ZMIN, XMAX, YMAX, and ZMAX define the borders of the super cell in crystal coordinates.)

Type	XMIN	YMIN	ZMIN	XMAX	YMAX	ZMAX
Unit cell	0	0	0	1	1	1
Double cell X	-1	0	0	1	1	1
Double cell Y	0	-1	0	1	1	1
Double cell Z	0	0	-1	1	1	1
Quadruple cell XY	-1	-1	0	1	1	1
2 x 2 x 2 cells	-1	-1	-1	1	1	1
3 x 3 x 3 cells	-1	-1	-1	2	2	2
4 x 4 x 4 cells	-2	-2	-2	2	2	2
To prevent atoms which are (nearly exactly) on edges or faces of the unit or super cell from being excluded during the filling procedure, an epsilon value is defined in the Epsilon input field in the Fill super cell dialog. This value will be subtracted from the XMIN, YMIN, and ZMIN values, and added to the XMAX, YMAX, and ZMAX values. If e.g. a super cell consisting of 3 x 3 x 3 = 27 cells is to be filled, the real dimensions are XMIN = YMIN = ZMIN = -1.01 and XMAX = YMAX = ZMAX = 2.01, if the default value of 0.01 for epsilon is used.

The filling of the unit cell is affected by the filter, which is described in details in the article "Filter: Overview".

By default, this function also generates the edges of the unit cell or all edges of and within the super cell automatically. If you do not want cell edges to be created automatically during this operation, switch off the Generate cell edges automatically checkbox.

Diamond will save the setting Generate cell edges automatically in its configuration file. That means, in all subsequent calls to a function that fills the unit cell or a super cell, no cell edges will be created automatically. To re-enable the automatic generation of cell edges, you must switch on the Generate cell edges automatically checkbox.

You can either make use of the OK button to fill the selected super cell, or use the Apply button, which does not close the dialog as OK does.

See also:

Filling the Unit Cell


Filling a Cell Range

While the previously described functions (filling the unit cell or a super cell), work with the unit cell or integer multiples of the unit cell only, you may define a parallelepiped by six distinct border values XMIN, YMIN, ZMIN, XMAX, YMAX, and ZMAX. These border values refer to one of three possible coordinate systems used in Diamond:

Crystal coordinates	The border values refer to the axes a, b, c of the unit cell. The values given (x/a, y/b, z/c) have no dimensions.
Reference coordinates	The border values refer to the axes of the reference coordinate system and describe a parallelepiped which is rectangular in any case, with values of dimension Angstroem.
View coordinates	The border values refer to the axes of the view coordinate system and describe a rectangular parallelepiped with dimension Angstroem, too.

To fill a cell range, choose the Cell range command from the Fill submenu of the Structure menu. This opens the Fill cell range dialog:

The filling of the cell range is affected by the filter, which is described in details in the article "Filter: Overview".

By default, this function also generates the edges within the given cell range automatically. If you do not want cell edges to be created automatically during this operation, switch off the Create cell edges automatically checkbox.

Diamond will save the setting Create cell edges automatically in its configuration file. That means, in all subsequent calls to a function that fills a cell range, no cell edges will be created automatically. To re-enable the automatic generation of cell edges, you must switch on the Create cell edges automatically checkbox.


Filling Boxes or Spheres Around Selected Atoms

If you want to fill a cell range but do not know suitable border values, you should make use of one of the following methods:

Filling a box around a selected atom

This fills a parallelepiped with border values referring to the crystal coordinate system or a rectangular parallelepiped referring to the reference or view coordinate system. The center is defined by the position of an atom, which has been selected from the parameter list. Such a parallelepiped is often called an enclosure box or simply a box.

To fill a box, choose the Box command from the Fill submenu of the Structure menu. This opens the Fill box dialog:

The radii of the box are defined by the three values given in DX, DY, and DZ. Their dimensions depend on the selected coordinate system:

Crystal coordinates	The radii refer to the axes a, b, c of the unit cell. The values given (x/a, y/b, z/c) have no dimensions.
Reference coordinates	The radii refer to the axes of the reference coordinate system and describe a parallelepiped which is rectangular in any case, with values of dimension Angstroem.
View coordinates	The radii refer to the axes of the view coordinate system and describe a rectangular parallelepiped with dimension Angstroem, too.

Filling a sphere around a selected atom

This fills a sphere around a center, which is defined by an atom of the parameter list. Such a sphere is often called enclosure sphere.

To fill a sphere, choose the Sphere command from the Fill submenu of the Structure menu. This opens the Fill sphere dialog:

The size of the enclosure sphere is limited by the two boundary values RMin and RMax in Angstroems.

Selection of the central atom

The central atom can be defined by a code or - more sophisticated - by selecting from the parameter list and - as far as necessary - from the list of symmetry matrices, Bravais translations and integer cell translations.

If neither symmetry operations nor translations are necessary, you can choose the central atom from the list Select center from parameter list. If you must use a symmetry-equivalent atom instead, you should make use of the Choose central atom dialog, which is opened from the Select center button.

Filter

The filling of the box or sphere is affected by the filter, which is described in details in the article "Filter: Overview".


Filling a Rectangular Area of the Screen

Both previously described functions (filling of a cell range or filling a box) may work with rectangular parallelepipeds with border values referring to the view coordinate system. But in most cases the border values in view coordinates are difficult to obtain, and thus an interactive method of filling an area is to be preferred. You define the X and Y coordinates of the parallelepiped by spreading a rectangular area on the screen (in the structure window). The border values in z-direction must then be given numerically.

Before you perform the filling of the rectangular area, the projection must be set to parallel. To ensure parallel projection, do the following:

1. From the Display menu, choose the Structure menu command.

2. On the Standard page of the Display structure dialog, check the parallel checkbox in the Projection group, if it has not yet been checked.

3. Close the dialog with OK.

To fill a rectangular area on the screen, choose the Area command in the Fill submenu of the Structure menu.

Alternatively you can use the [image] button in the Build toolbar.

(The mouse cursor changes to a special symbol indicating that the "Fill area mode" is now active. You can cancel this mode simply by pressing the Escape button or by choosing the Area command from the menu or from the toolbar once again.)

To fill the contents of a rectangular area, do the following steps:

1. Move the mouse cursor to the upper left corner of the desired position of the rectangular area.

2. Press down the left mouse button, and (with mouse button down) move the mouse cursor to the lower right corner of the area.

3. Release the left mouse button, when you have reached the desired position.

4. In the Fill cell range dialog, define ZMin and ZMax (you may also alter the values for XMin, YMin, XMax, and YMax, if necessary), then press OK.

The calculation of the values XMin, YMin, XMax, and YMax considers the current orientation as well as the current position of the structure picture in the structure window and the current enlargement factor. The z values refer to the origin of the unit cell, that means (0,0,0) in both crystal and reference coordinates. See the chapters "Orientation..." and "Projection: Overview" about orientation of the structure, projection and enlargement factor.

The filling of the rectangular area is affected by the filter, which is described in details in the article "Filter: Overview".


Generating Atoms Directly: Overview

While the generation of atoms within a well-defined range of the crystal structure lattice is a quite suitable way to get an overview, atoms can be generated directly by applying the corresponding atom code.

In most cases the purpose of generating special atoms by code is to create one or more atoms which serve as starting atom of a more complicated inorganic framework or as starting point for molecules. This kind of intialization of the structure picture is mostly followed by functions which complete coordination spheres subsequently or complete fragments. (See the articles "Spheres: Overview" and "Molecules: Overview".)

In Diamond, you can specify the atoms to be generated by codes or code ranges or - more sophisticated - by selecting atoms from the parameter list and - as far as necessary - symmetry matrices, Bravais translations, and integer cell translations. This is done with the Add atoms dialog, which is described in details in "Adding Some Atoms from Parameter List".

If the atomic parameter list describes one or more complete molecules, e.g. a protein which has been imported from Protein Data Bank, the Add all atoms command can be used to transform all atoms from the parameter list immediately without applying any symmetry operations. See "Adding All Atoms of Parameter List".

See also:

Atom Codes

Created Atoms


Adding Some Atoms from Parameter List

Diamond offers the comprehensive Add atoms dialog, where you can specify the atoms to be generated by codes or code ranges or - more sophisticated - by selecting atoms from the parameter list and - as far as necessary - symmetry matrices, Bravais translations, and integer cell translations.

To open the Add atoms dialog, choose the Add atoms command from the Structure menu.

Alternatively you can use the [image] button in the Build toolbar.

There are two different ways to define the codes of the atoms you want to be generated:

1. Define the codes directly using the ORTEP-like atom codes. If you are familiar with this kind of coding atoms, you can enter the code(s) in the input field Code(s), and then start the generation with OK or Apply.

2. Define the codes indirectly using the list of atomic parameters, symmetry operations, Bravais translations and the input fields for the ranges of integer cell translations, and then start the generation with OK or Apply.

(You may combine these two methods, that means you may select atoms from the lists and additionally specify codes.)

Selecting atoms and symmetry operations

All lists in the Add atoms dialog work with extended selectionref_listextendedsel. To generate one or more atoms, do the following steps:

1. In the list Atoms from parameter list, select the atom(s) you want to be generated.

2. In the lists Symmetry operations and Bravais translations, select the symmetry matrices and Bravais translations, rsp. If no symmetry operation is to be applied, select "x,y,z" and "+(0,0,0)", rsp. (which is the default setting in these lists). If needed, multiple symmetry operations and/or multiple Bravais translations can be applied to the selected atom(s).

3. In the six input fields below, enter the integer cell translations, as far as needed. If you need not apply cell translations, leave these fields untouched. (The default values when opening the dialog are 0 for all cell translations.)

4. Start the generation of the atoms by closing the dialog with OK. If you want to generate more atoms subsequently, you should use the Apply button instead, since this does not close the dialog. (Use the Reset selections button, if you want to reset the settings.)

Defining atom codes

1. Enter the atom codes into the input field Code(s). Atom codes may be defined as single, multiple codes (separated by commas, semicolons or blanks) or as code ranges.

Example: "3454011-4556042" creates atoms with numbers #3 through #4 (positions in the parameter list; first position is #1) and applies the symmetry operations #1 through #4 and Bravais translations #1 through #2 as well as the integer cell translations -1 <= x <= 0 and -1 <= z <= 1 to these atoms. This code range will generate 2 * 4 * 2 * 2 * 3 = 96 atoms.

2. Start the generation of the atoms by closing the dialog with OK. If you want to generate more atoms subsequently, you should use the Apply button instead, since this does not close the dialog.

Filter will not be used

When Diamond generates atoms from the Add atoms dialog, the settings in the filter (see "Filter: Overview") will not be taken into account.

Multiple atoms on special sites

When generating atoms via the Add atoms dialog, Diamond does not check, if multiple atoms are generated on one and the same position. This may happen, if you apply multiple symmetry operations to one or more atoms on special sites.

See also:

Atom Codes

Created Atoms


Adding All Atoms of the Parameter List

Crystal structure descriptions of molecular structures often contain the coordinates of those atoms, that together just describe a molecular unit. To get a complete molecule only these atom positions are needed, that means the application of symmetry operations is not necessary. This strategy can save much time for calculation, especially with very large structures (e.g. proteins).

To add all atoms from the parameter list, choose the Add all atoms command from the Structure menu.

Alternatively you can use the [image] button from the Build toolbar or use the accelerator key Shift+Ctrl+A.

If the atomic parameter list contains N atoms with valid coordinates, this procedure creates N atoms directly without applying symmetry operations, Bravais translations, and integer cell translations. That means, all N atoms have the code A555011.

Like for the generation of atoms from the Add atoms dialog, the settings of the filter (see "Filter: Overview") will not be taken into account.


Generating Bonds: Overview

The current version of Diamond does not support direct bonding information in the structural input parameters. That means, since there is no equivalent to the atomic parameter list, whereas each created atom can be reduced to a definite atom of the parameter list, bonds cannot.

There are three different ways to generate bonds between generated atoms:

1. Automatic generation when atoms are generated

Atoms are connected automatically when surrounding atoms in coordination spheres or molecules are created. For details, see the chapters "Spheres: Overview" and "Molecules: Overview", rsp.

2. Connecting atoms on demand

All or selected atoms are connected with each other on command, e.g. after the atoms of the unit cell has been generated. This is described in "Connecting All or Selected Atoms".

Both methods work with the connectivity list, which defines what atoms may be connected.

3. Inserting bonds manually

Two selected atoms can be connected independent from the current settings in the connectivity list, that means even the strongest bonding geometry can be forced. The article "Inserting a Bond Between Two Atoms" describes how to insert bonds manually.


Connecting All or Selected Atoms

This article describes how some or all created atoms can be connected with each other basing on the bonding criteria, which are currently defined in the connectivity list.

Please note that Diamond additionally offers several functions that generate bonds automatically when atoms in coordination spheres surrounding selected atoms or when molecules are generated. For details, see the chapters "Spheres: Overview" and "Molecules: Overview", rsp.

To connect atoms with each other, choose the Connect atoms command from the Structure menu, or push the [image] button in the Build toolbar, or use the accelerator key Shift+Ctrl+N.

Connecting all atoms of the structure picture

The connecting function applies to all created atoms, if no atom is currently selected. This means, all atoms of the structure picture will be connected with each other, provided that the atom type combinations (the bond types) are (a) enabled for bonding and (b) if the interatomic distances are within the bonding spheres.

Connecting selected atoms with each other

If two or more atoms are selected, only these selected atoms will be connected with each other, provided that the atom type combinations are (a) enabled for bonding and (b) if the interatomic distances are within the bonding spheres.

Creating bonds which are not enabled in the connectivity list

As stated above, the bonding criteria are derived from the connectivity list. If you must connect atoms, which are not presently enabled in the current connectivity list, you have two possibilities:

A. If there is only a few amount of atoms to be connected, you can insert the bonds manually, using the method that is described in the next article "Inserting a Bond Between Two Atoms".

B. If a rather large amount of atoms is to be connected, use the following way:

1. From the Structure menu, choose the Connectivity command to open the Connectivity dialog.

2. In the Connectivity dialog, enable the atom type combination for bonding in the list Select atom type pair(s) to be connected. (This will select the atom type combination in the Bonding sphere combobox and show the histogram of distances.)

3. Change the bonding sphere if necessary either by editing the values for DMin or DMax or by shifting the red lines in the histogram.

4. Push the Connect button. This will connect all atoms with each other (or the selected atoms, rsp.) basing on the current setting of the connectivity list.

5. Close the Connectivity dialog using the Cancel button to leave the previous settings for the connectivity list unchanged.

Adjusting structure picture to current connectivity

Changes in the connectivity list do not reflect existing bonds. This means, a bond will not be destroyed automatically, if the corresponding atom type combination becomes disabled for bonding or if the bonding sphere becomes shorter or longer than the actual interatomic distance. (In similar way bonds will not automatically be created on changes of the connectivity list.)

If you must get rid of bonds, which are not more enabled by the connectivity list, you have to delete them manually. The most appopriate way to adjust the structure picture to the current connectivity list, is to delete all bonds first, then to call the Connect function:

1. If the data sheet or a list is active in the secondary pane, click into the structure picture with the mouse. (This is necessary to set the input focus to the main pane.)

2. From the Edit menu, choose the Select all command. This will mark all objects as selected.

3. Click into one of the selection markers, and choose the Bonds command from the Destroy submenu of the context menu. This will selectively destroy only the bonds, but leave all other selected objects, such as atoms or labels, unchanged.

4. Click into the structure picture. This will reset all selections.

5. From the Structure menu, choose the Connect atoms command. This will connect all atoms with each other basing on the current connectivity list.


Inserting a Bond Between Two Atoms

A bond can be inserted between two selected atoms, independent from the connectivity list. This enables to create bonds that may have no chemical meaning.

Diamond supports two different modes to insert one or more bonds between two selected atoms each. The first mentioned mode is to select the two atoms, and then executing the command to insert the bond. The second mode enables you to select two atoms each, which will then automatically be connected. This mode is continued unless you end it.

Follow these steps to insert a bond between two atoms:

1. Click on the two atoms, which are to be connected, one after the other.

2. Push the [image] button in the Build toolbar.

Follow these steps to create multiple bonds:

1. From the Structure menu, choose the Insert bonds command. The mouse cursor will change its symbol.

2. Click on two atoms, which are to be connected, one after the other.

3. Repeat these two steps, if you want to connect other atom pairs.

4. To end this mode, choose the Insert bonds command again or simply press the Esc key.

The design of the new bonds is copied from the design of the corresponding bond type, and can be changed after bond creation (like every bond may be edited individually). See the article "Designing Selected Bonds".


Spheres: Overview

Diamond uses two different kinds of spheres, often called "enclosure spheres", to generate atoms within a spherical environment of a central atom. The simplest one is called "fixed sphere", since it is simply defined by a minimum and maximum radius value. The other one is called "coordination sphere", since the size of that kind of sphere depends on the connectivity and thus varies from atom type to atom type. For details, see the article "Fixed vs. Coordination Spheres".

"Filling Fixed Spheres" describes how to fill a fixed sphere around one or more selected atoms, whereas the articles "Filling Coordination Spheres Around Selected Atom Types", "Filling Coordination Spheres Around Selected Atoms", and "Filling Coordination Spheres in Multiple Cycles" explain how coordination spheres can be filled.

The last article of the "Spheres" chapter, "Creating Broken-off Bonds", shows how so-called "broken-off" bonds can be created to display infinitesimal bonding.


Fixed vs. Coordination Spheres

Diamond distinguishes between two kinds of spheres to generate atoms within a spherical environment of a central atom:

1. Fixed spheres

This kind of sphere is called "fixed" because its dimension is simply defined by a minimum and a maximum radius value. This means, if you fill a fixed sphere around a central atom, Diamond will create all atoms that have a distance from the central atom of at least the minimum radius value but not more than the maximum radius value. These values have the dimension Angstroems in Diamond.

2. Coordination spheres

This kind of sphere is called "coordination sphere" because it is used to generate neighbouring atoms which are connected with the central atom. Since these bonding spheres depend on the atom types of the atom in the center and the atom to be generated, the size of this kind of sphere varies and is not fixed. Thus "coordination spheres" are sometimes called "generic spheres" in Diamond.

When filling coordination spheres, a new atom will only be created, if the atom type of that new atom is connected with the central atom and the distance lies within the bonding sphere range. These settings are defined in the connectivity (compare "Connectivity"). Central atom and new atom will be connected with a bond corresponding to the settings for the bond type defined for the atom type combination (compare "Bond Types").

Please note that atoms may be not created, if the Filter function has been activated. To get more information about the Filter function, read the article "Filter: Overview".


Filling Fixed Spheres

To generate atoms within fixed spheres, use the following two steps:

1. Select the atoms which become centers of the fixed spheres. If no atom is selected, every atom will be taken as central atom.

2. Define the dimensions of the fixed sphere and start the generation of atoms. To do this, choose the Spheres command from the Structure menu. This will open the Define fixed sphere dialog where you can change the minimum (RMin) and maximum (RMax) radius values in Angstroems. The generation of atoms will be started with the OK button.

Diamond stores the latest minimum and maximum radius values in its configuration file, so that you can easily repeat the generation of atoms using the [image] button from the Build toolbar. This will generate atoms directly without calling the Define fixed sphere dialog, using the latest minimum and maximum values.

Please note that atoms may be not created, if the Filter function has been activated. To get more information about the Filter function, read the article "Filter: Overview".


Filling Coordination Spheres Around Selected Atom Types

The generation of atoms within coordination spheres can be performed in different ways. This article describes how coordination spheres around central atoms belonging to selected atom types are filled with atoms belonging to other selected atom types.

To fill coordination spheres around selected atom types, choose the Coordination spheres command from the Structure menu. This will open the Fill coordination spheres dialog:

Choose the atom type(s) which shall become centers of coordination spheres in the Central atom list, and the atom type(s) of the atoms to be generated in the Ligand atom list. Leave the Number of cycles input field 1, unless you want to fill coordination spheres in multiple cycles (compare "Filling Coordination Spheres in Multiple Cycles"), and do not check the checkbox Create broken-off bonds, unless you want to create "broken-off" bonds (compare "Creating Broken-off Bonds").

To start the generation of atoms within the coordination spheres, either press the OK button, which will close the dialog, or press the Apply button, which does not close the dialog and has the advantage that you can repeat the procedure with the same or other atom types.

A new atom will only be created in this procedure, if:

(1) its atom type belongs to the atom types selected in the Ligand atom list,

(2) the atom type of the central atom belongs to the atom types selected in the Central atom list,

(3) the atom type combination (bond type) is enabled for being connected with a bond in the connectivity list,

(4) the distance between new atom and central atom lies within the range of the bonding sphere, which is also defined in the connectivity list,

(5) the new atom is not blocked by the Filter function (compare "Filter: Overview").

If atoms have been selected, that selection will be ignored within this procedure.


Filling Coordination Spheres Around Selected Atoms

While the previously described procedure (compare "Filling Coordination Spheres Around Selected Atom Types") ignores the current selection of atoms but takes all atoms belonging to selected atom types as central atoms, this article describes how to take the currently selected atoms as centers of coordination spheres only.

To fill coordination spheres around selected central atoms, first select the atoms. If no atom is selected, every atom will be taken as central atom.

To start the generation of atoms, either press the [image] button in the Build toolbar or use the "hotkey" Shift+Ctrl+S.

A new atom will only be created in this procedure, if:

(1) the atom type combination (bond type) of central atom and new atom is enabled for being connected with a bond in the connectivity list,

(2) the distance between new atom and central atom lies within the range of the bonding sphere, which is also defined in the connectivity list,

(3) the new atom is not blocked by the Filter function (compare "Filter: Overview").

Please note:

If you have previously generated atoms around selected atom types (compare "Filling Coordination Spheres Around Selected Atom Types"), the selection of atom types in the Fill coordination spheres dialog will be ignored.


Filling Coordination Spheres in Multiple Cycles

A common procedure is the stepwise construction of coordination spheres especially in 3D frameworks or layers of inorganic structures. That means you first create atoms within the coordination spheres of selected central atoms and then repeat this procedure for the just created atoms and so on.

The stepwise filling of coordination spheres can be done in three different ways:

1. By clicking on the [image] button in the Build toolbar or pressing the Shift+Ctrl+S key combination for each step.

2. By choosing the Coordination spheres command from the Structure menu and using the Apply button in the Fill coordination spheres dialog.

3. By using a number greater than one in the input field Number of cycles in the Fill coordination spheres dialog.

Example: Building up the 3D framework of Hittorf violet phosphorus, starting with one atom of the parameter list (upper left), and then calling the coordination sphere function five times, leading to the picture right above. Applying the coordination sphere function again with a number of cycles of ten leads to the picture below.

If you build up coordination spheres stepwise without using the Fill coordination spheres dialog (method #1), you should ensure that no atom is selected. In the first step the coordination spheres of all atoms will be filled, while in the second step all coordination spheres of the atoms that have been created in the first step will be created, and so on.

If you use method #3, Diamond swaps the selection of atom types for central atoms and ligand atoms after each step. For example, if you have selected "Si" as central atom and "O" as ligand atom, and a cycle number of 3, in the first cycle all O atoms in the coordination spheres of all Si atoms will be created, while in the second cycle all Si atoms will be created in the coordination spheres of all O atoms. The third cycle will work like the first cycle, that means Si as central atom.


Creating Broken-off Bonds

The so-called "broken-off" bonds are usually used to display an infinitesimal framework, that means especially for inorganic 3D frameworks or layer structures.

To create broken-off bonds, choose the Coordination spheres command from the Structure menu. In the Fill coordination spheres dialog, select the atom types for central atoms as well as the atoms to be generated, and check the Create broken-off bonds checkbox. Then press the OK or Apply button to start the generation of broken-off bonds.

When Diamond generates broken-off bonds, the created atoms become the attribute "invisible". Each time Diamond draws a bond between a visible and an invisible atom, this will be shortened to 0.35 of its normal length.

Example: Contents of the unit cell of alpha quartz (left) with Si in cyan and O in red color. The second picture shows the next Si neighbours of the O atoms, whereas the right picture shows broken-off bonds to these Si atoms instead.

If you use a Number of cycles greater than one, only those atoms become invisible that are generated in the last cycle.

Manual creation of broken-off bonds

You can manually assign the attribute "invisible" to one or more atoms with the help of the Edit atoms dialog. See the article "Designing Selected Atoms" how to edit the attributes (the design) of one or more selected atoms. Bonds to such invisible atoms will then become automatically broken-off bonds.

Resetting broken-off bonds to normal bonds

You can reset broken-off bonds to normal bonds by resetting the "invisible" attribute of the corresponding atoms. Please note that the "invisible" attribute may be changed automatically, if you edit atom types with the "Update created atoms" flag switched on.


Molecules: Overview

This chapter describes how molecules can be created from the parameter list or how molecular fragments can be completed.

The first articles show you how the molecular generator of Diamond works and how to process infinite structures or macromolecules:

How the Molecular Generator Works

Special Settings for the Molecular Generator.

The following article describes how molecules can be generated from the atomic parameter list:

Generating Molecules from Parameter List.

The last articles of this chapter will tell you how to complete molecular fragments (for example the contents of the unit cell), and how to create packing diagrams:

Completing Molecular Fragments

Packing Diagrams.


How the Molecular Generator Works

The creation of molecules is comparable with the cyclic filling of coordination spheres. For molecules the number of cycles is in principle unlimited, and the procession will stop after the last atom of each molecule has been created.

That means if you have for example created the contents of the unit cell, and then apply the molecular generator, Diamond completes the coordination spheres for every atom, and in every further cycle it completes the coordination spheres of the atoms that have been created in the cycle before.

If the structure has infinite parts, what is the case in most of the inorganic structures, the molecular generator would not come to an end. To avoid this, Diamond offers several settings to bring the generation of molecules to an end. These settings are described in the following article "Special Settings for the Molecular Generator".

If you apply the molecular generation to typical inorganic frameworks, for example to sodium chloride, the results are unpredictable.

You can stop the molecular generator with the Ctrl+Break key combination.

Please note that a proper setting of the connectivity is an essential requirement for the molecular generator. Otherwise a structure may become infinite, although it has isolated molecules, if "wrong" bonding spheres have been defined. To check the connectivity, choose the Connectivity command from the Structure menu.


Special Settings for the Molecular Generator

Diamond offers settings to limit the molecular generator for macromolecules that are "too big" or to infinite structures.

1. The number of recursions can be limited to a maximum number of cycles during the recursive filling of coordination spheres.

2. Security borders, which can have the shape of spheres, boxes or parallel epipeds, can be defined to stop the generation of molecules at well-defined borders. These security borders are called "cage" in Diamond.

To edit the settings for the molecular generator, choose the Molecule cage command from the Structure menu. This opens the Molecule cage dialog:

The input field Maximum depth of recursion defines the number of cycles Diamond uses to create the atoms in the coordination spheres of those atoms that have been created in the previous cycle. If this number is reached during a molecular generation process, the structure may be polymeric. The maximum value is 128. If the number is too small or the molecule is too big or the structure is really infinite, you can call the molecular generator again starting with the previously created molecular fragment. For more details how to complete molecular fragments, see the article "Completing Molecular Fragments".

The other settings define the security borders. Diamond uses three kinds of security borders ("cages"):

Crystal cage	Defines a parallel epiped with border values refering to the crystal coordinate system. The six border values are defined in the corresponding input fields XMIN, YMIN, ZMIN, XMAX, YMAX, and ZMAX. If the checkbox Active is checked, the molecular generator will stop for atoms outside these borders. Otherwise the crystal cage will be ignored.
Cartesian cage	Defines a rectangular parallelepiped similar to the crystal box described above but with borders refering to the reference coordinate system (in Angstroems).
Spherical cage	Defines a sphere with center at XC, YC, ZC and the inner and outer bound RMIN and RMAX, rsp. (in Angstroems).

Boxes and sphere may be activated independent from each other. The molecular generator will stop searching for neighbours, if an atom found lies outside at least one of these bodies. Atoms outside the boxes and/or sphere will be created but do not serve as starting point for a search for neighbours.


Generating Molecules from Parameter List

Diamond offers two strategies to create one or more molecules from the atoms in the parameter list:

(1) By adding all atoms of the parameter list without applying any symmetry operations. This is the method of choice if the atomic parameter list describes one or more entire molecules.

(2) By creating molecules from every atom of the parameter list applying symmetry operations automatically if necessary. This is the question of choice, if the parameter list does not describe complete molecules, for example if the molecules have internal symmetry.

To create molecules directly from the atomic parameter list (method #1), do the following steps:

1. From the Structure menu, choose the Add all atoms command, or use the "hotkey" Shift+Ctrl+A, or press the [image] button in the Build toolbar.

2. Check the connectivity settings for the creation of bonds which follow in the last step. Compare the article "Connectivity" how to check or change the connectivity.

3. From the Structure menu, choose the Connect atoms command, or use the "hotkey" Shift+Ctrl+N, or press the [image] button in the Build toolbar.

If you do not know if the atomic parameter list describe complete molecules or if you know definitely that molecules have internal symmetry elements and the atomic parameter list contains the asymmetric parts only ("asymmetric unit"), you must use method #2. To create molecules from the parameter list, do the following steps:

1. Check the connectivity settings.

2. From the Structure menu, choose the Molecules command, or use the "hotkey" Shift+Ctrl+M, or press the [image] button in the Build toolbar.

Method #2 is the secure method, since it applies symmetry operations to create the symmetry equivalent parts of the molecules from the asymmetric unit. When Diamond generates molecules from the parameter list, it uses the following procedure:

1. For the first atom in the parameter list, create an atom without applying any symmetry operation. That means the first created atom will have the atom code "1555011".

2. With this atom as starting point, call the molecular generator. This will recursively fill the coordination spheres around the starting atom.

3. Repeat these steps for the next atom of the parameter list, but only if that atom or a symmetry equivalent atom has not yet been created.

If the atomic parameter list describes one complete molecule, step #3 will create no further atom, since all atoms of the molecule have been created in step #2. If the atomic parameter list contains more than one molecule, step #3 will be called only as often as molecules are in the parameter list.

The following example shows a molecule of cytochrome C (from rice embryos (ORYZA SATIVA L); Protein Data Bank entry code 1CCR), which has been created using method #1. Method #2 would lead to the same result:

Another example uses the gamma modification of cyclo-octasulfur from the Inorganic Crystal Structure Database (Collection Code: 66517). The structural parameters from the data sheet are:

Bibliographic data

Name

Cyclo-octasulfur - γ

Formula

S8

Author(s)

Gallacher, A C, Pinkerton, A A

Title

A redetermination of monoclinic γ-Sulfur

Journal

ACSCEE 49 (1993), pp. 125 - 126

Crystal data

Formula sum	S8

Crystal system	monoclinic

Space group	P 1 2/c 1 (no. 13)

Unit cell dimensions	a = 8.4375(30) Å

b = 13.000(2) Å

c = 9.250(3) Å

β = 124.50(3) °

Cell volume	838.80(1725) Å3

Z	4

RAll	0.036

Pearson code	mP32

Formula type	N

Wyckoff sequence	g8

Atomic coordinates

Atom	Ox.	Wyck.	x	y	z

S1	+0	4g	0.64844(20)	0.34375(10)	0.32422(20)

S2	+0	4g	0.80859(10)	0.57813(10)	0.4707(1)

S3	+0	4g	0.74219(20)	0.44141(10)	0.53125(10)

S4	+0	4g	0.58203(20)	0.67578(10)	0.38281(10)

S5	+0	4g	0.07959(20)	0.79688(10)	0.19922(20)

S6	+0	4g	0.24219(20)	0.03088(10)	0.21973(20)

S7	+0	4g	0.30664(20)	0.89063(10)	0.34961(20)

S8	+0	4g	0.14746(20)	0.12695(10)	0.32813(20)

The atomic parameter list contains eight sulfur atoms, but using method #1 leads to the result (left part of the picture below), whereas method #2 leads to the right picture, which shows two molecules with eight atoms each. The atoms in the parameter list above describe only the asymmetric parts of the two molecules:

The list of created atoms for the right picture contains the following atoms:

4	S1	1555011	x, y, z	 0.64844 0.34375 0.32422

5	S1	1655021	1-x, y, 0.5-z	 0.35156 0.34375 0.17578

6	S3	3555011	x, y, z	 0.74219 0.44141 0.53125

7	S3	3655021	1-x, y, 0.5-z	 0.25781 0.44141-0.03125

8	S2	2555011	x, y, z	 0.80859 0.57813 0.47070

9	S2	2655021	1-x, y, 0.5-z	 0.19141 0.57813 0.02930

10	S4	4555011	x, y, z	 0.58203 0.67578 0.38281

11	S4	4655021	1-x, y, 0.5-z	 0.41797 0.67578 0.11719

12	S5	5555011	x, y, z	 0.07959 0.79688 0.19922

13	S5	5555021	-x, y, 0.5-z	-0.07959 0.79688 0.30078

14	S7	7555011	x, y, z	 0.30664 0.89063 0.34961

15	S7	7555021	-x, y, 0.5-z	-0.30664 0.89063 0.15039

16	S6	6565011	x, 1+y, z	 0.24219 1.03088 0.21973

17	S6	6565021	-x, 1+y, 0.5-z	-0.24219 1.03088 0.28027

18	S8	8565011	x, 1+y, z	 0.14746 1.12695 0.32813

19	S8	8565021	-x, 1+y, 0.5-z	-0.14746 1.12695 0.17188


Completing Molecular Fragments

Many of the functions that generate atoms within a given cell range leave molecular fragments if the structure contains molecular units. These molecular units are incomplete because the generation of atoms has stopped at the border values of the cell range, while Diamond does not complete the residuals to complete molecules automatically.

You can either complete molecules starting from selected atoms only, or complete all fragments, if no atom has been selected.

Before you start the molecular generator ensure that the connectivity settings for the current structure have been properly checked. See the article "Connectivity" how to check the connectivity.

To complete one molecular fragment, select one or more atoms of the fragment and then choose the Complete fragments command from the Structure menu or use the "hotkey" Shift+Ctrl+F or press the [image] button in the Build toolbar.

To complete all molecular fragments, ensure that no atom is selected (click at an arbitrary position of the structure picture but not on an object), and then continue as described for single fragments.

The following two illustrations show the Keggin structure from the Inorganic Crystal Structure Database (ICSD Collection Code: 908). The upper illustration shows the contents of the unit cell with one phosphorus atom selected (left picture), which serves as starting point for the completion of a fragment that leads to the right picture:

The following picture shows the result of the application of the same function to all atoms of the unit cell. (No atom has been selected before the Complete fragment function has been called.):

The most common application of this function is the generation of packing diagrams, which are described in the following article "Packing Diagrams".


Packing Diagrams

Packing diagrams show the orientation of molecules to each other in the unit cell. With the help of the molecular generator Diamond offers in principal two strategies to create packing diagrams:

(1) Create all atoms in the unit cell. Then complete all molecular fragments. This procedure generates all molecules that lie at least in parts inside the unit cell.

(2) Create as many molecules as are defined in the unit cell. In most cases, the number of molecules corresponds with the number of formula units in the unit cell (Z).

The following illustration compares the results of these two methods. The picture in the upper left shows one molecule that has been created with the Molecules command from the Structure menu. (The cell edges have been added manually; compare "Adding Cell Edges".) The picture in the upper right shows the packing of two molecules and has been created using method #1, whereas the picture below, which has been created using method #2, shows a total of even eight molecules.

Reference from the data sheet:

Name

3BETA-ACETOXY-5BETA,6BETA-N-NITRO-AZIRIDINYL-CHOLESTENE (AT -98 DEG.C)

Formula

C29 H48 N2 O4

Author(s)

HAIRE M J   , HARLOW R L

Journal

JOCEA 45 (1980), pp. 2264 - 2264

The creation of a packing diagram after method #1 is described in the previous article "Completing Molecular Fragments".

To create a number of molecules defined by the Z-value and if the parameter list describes one molecule, follow these steps:

1. Use the filter function to select one atom from the parameter list, which shall serve as starting atom for the molecular generator. See the article "Filter: Overview" how to select atoms in the filter function.

2. "Fill" the contents of the unit cell. Since the filter is active, only the Z symmetry equivalent atoms of the starting atom will be created in that process. See the article "Filling the Unit Cell" how to generate the contents of the unit cell.

3. Switch the filter off (click on the [image] button), check the connectivity, if not yet done, and then complete the Z generated atoms to Z molecules.

This may lead to a picture like above. Note that some molecules may extend the borders of the unit cell while some atoms inside the unit cell will not be created.


Inserting an Atom

You can define a new atom in the center of two or more selected atoms. Therefore a new atom will be added to the atomic parameter list as "Dummy" atom.

The most common uses of inserting an atom is to use a dummy atom for example in the center of a cyclopentadienyl ring, like in the following picture:

Reference:

Author(s)

van der Zeijden, Adolphus A. H., Mattheis, Chris, Fröhlich, Roland

Title

[1,2-Di(methoxyethyl)-h5-cyclopentadienyl]trichlorozirconium(IV)

Journal

Acta Cryst. (1998). C54, 458 - 460

To define a dummy atom - for example in the center of a cyclopentadienyl ring -, follow these steps:

1. Build up the structure as described in the previous chapters. (For the above example, make use of the molecule function.)

2. Select the five C atoms of the cyclopentadienyl ring, and then choose the Insert atom command from the Structure menu. This will open the Insert atom dialog, like in the following example:

3. Change the atom symbol, which is "Dummy" by default (or "Dummy2" for the second dummy atom, etc.), if you want, and then confirm with OK.

4. Choose the Atom types command from the Edit menu, which opens the Atom types dialog, if you want to change the shape of the dummy atom. (See "Designing Atoms and Atom Types: Overview" how to edit atom types.)

How to connect the dummy atom with the praseodym atom like in the picture, see the article "Inserting a Bond Between Two Atoms". To make the bond "fragmentated", read the article "Fragmentated Bonds".

Another important application of dummy atoms is in the centers of coordination polyhedra, where no atom has been defined in the parameter list. This is treated in the article "Polyhedra With No Central Atom".


Dismantling: Overview

Functions for the controlled dismantling of structural parts are almost as important as functions for building up structures. Many of the dismantling functions can be found in the Destroy submenu of the Structure menu:

The following articles will describe in details

- how to delete selected molecules or fragments (that means how to cut off parts of molecules),

- how to delete selected atoms or bonds,

- how to destroy the entire structure picture.


Deleting Atoms or Bonds

Diamond offers a lot of ways to delete atoms or bonds:

1. Using the Delete key

This is the most common method to delete one single or multiple atoms and/or bonds. First select the atom(s) and/or bonds, rsp., then hit the Delete key. See the article "Selecting Objects" how to select atoms and bonds.

2. Using commands from the context menu

If multiple kinds of objects have been selected (e.g. both atoms and bonds that have been selected inside a mouse-defined rectangle), but you want to delete selectively atoms or bonds only, choose the appropriate command from the Destroy submenu of the context menu. To open the context menu for the selected objects, click into one of the objects with the right mouse button. This selective deleting does not touch any selected objects of other kinds.

3. Deleting atoms or bonds from the atom or bond list

If you want to delete atoms and the atom list is active in the data pane, or if you want to delete bonds and the bond list is active in that pane, you can choose the Destroy atom(s) or Destroy bond(s) command, rsp., to delete all selected atoms or bonds, rsp.

4. Deleting using enhanced selections

The lists in the data pane offer comprehensive methods to select atoms and bonds for very special criterions. This selection works in principle like that:

(1) Open the atom list, if you want to delete atoms.

(2) Sort the atoms for a suitable criterion.

(3) Select the atoms in the list. This is easy if these atoms are arranged in a block due to a suitable sort criterion.

(4) Continue like in method #3.

5. Deleting all created atoms belonging to selected atoms or atom types

You can use the list of atom types or atomic parameters instead of the list of created atoms to select and delete all atoms that belong to selected atoms from the parameter list or selected atom types:

(1) Open the atom type list or the atomic parameter list. (Choose the appropriate command from the List submenu in the Display menu.)

(2) If necessary, sort the list. This may be suitable in large atomic parameter lists, where you mostly sort for element symbols.

(3) Select the atoms or atom types in the list.

(4) Choose the Select atom(s) command from the context menu of the list. This selects all atoms belonging to the selected atoms or atom types, rsp., in the structure picture.

(5) Click with the right mouse button into one of the selected atoms in the structure picture, and then choose the Destroy atom(s) command from the context menu.

6. Deleting all created bonds belonging to selected bond types

This works like method #5, but with the list of bond types in the data pane, and with commands like Select bond(s) and Destroy bond(s) instead.

7. Deleting all bonds with a selected bond length

One special application of method #6 is to select and delete all bonds with lengths within a well-defined distance range. For that, choose the bonds command from the List submenu of the Display menu to show the bond list in the data pane. Sort the bonds for bond lengths, and select a block of bonds having the desired bond lengths. Then choose the Destroy bond(s) command from the context menu of the bond list.

8. Deleting all non-bonded atoms

Diamond offers a special command that deletes all non-bonded atoms. This command is mostly used to remove solvation molecules from structure pictures showing molecules. To delete all non-bonded atoms, choose the Non-bonded atoms command from the Destroy submenu of the Structure menu, or push the [image] button in the Build toolbar.

There are also commands to delete complete molecules or fragments of molecules.


Deleting Molecules or Fragments

You can delete a complete molecule with one mouse-click or a fragment of a molecule with two mouse-clicks.

To delete a molecule, select an atom of the molecule, and then choose the Molecules command from the Destroy submenu of the Structure menu (or the same command in the context menu). Instead, you can use the [image] button in the Build toolbar.

Deleting a fragment means that you destroy a bond within a molecule and then delete the cut part. To delete a fragment, first select the atom at the residual side of the bond, and then select the atom at the fragment that will be discarded. Then choose the Fragment command from the Destroy submenu of the Structure menu.


Destroying the Structure Picture

You can simply discard the entire contents of the structure picture (except user-defined text) with the All command from the Destroy submenu of the Structure menu, or with the "hotkey" Shift+Ctrl+D.

This command deletes the entire structural part, that means all created atoms and thus all bonds between them, cell edges and coordination polyhedra. Text(s) in the structure window (but not labels) will remain.


Display of Structure Picture: Overview

This section informs you about the versatile possibilities to represent a structure in Diamond. It will provide answers for the following main questions:

•	What is the difference between rendered representation, and standard ("flat") representation?

•	Which models can be used?

•	What is double buffering?

•	What is the difference between page view, print preview, and standard view?

•	How to define and change the orientation of the structure?

•	How is the structure projected? (What about perspective, enlargement factor, and stereo representation?)

•	How do I define light sources?

•	How can I change the background color? (And what is black-on-white mode?)

•	What about other effects such as depth cueing, shading edge, front emphasizing, bond tapering, and overall radius factor?

•	How can I change the colors, radii, and other details of the atoms and bonds?

•	What can I use alternative color differentiations for?

•	How do I define, design, or destroy cell edges?

•	How do I create, design, or destroy coordination polyhedra?

•	What about ORTEP-like representation of displacement parameters as ellipsoids?

•	How can I label atoms and bonds?

•	What about user-defined text in the structure picture?

•	What about the legend of atom types?

•	What about the coordinate system that shows the current orientation?

•	How can I optimize the structure picture?


Rendered Representation: Overview

The version 2.0 of Diamond introduced a new way of representing a structure picture producing high-quality graphics with shaded objects, transparency, material and light properties. This is called the "rendered representation", whereas the "old" standard representation, which is of course still available, will be called "flat representation" instead.

The following article will describe the differences between these two kinds of representation, their advantages and disadvantages, depending on the application of the picture or printout, as well as limitations.


Rendered Representation: Features and Limitations

Diamond uses the MS Windows implementation of the OpenGL graphics library for rendered representation. This gives you a lot of possibilites to display photo-realistic shaded models with user-defined light sources, materials properties and optional transparency if wanted. Of course the common old-style drawing mode (the flat representation), which is more useful for black-on-white printouts, is also supported. The following illustration compares flat (left) and rendered (right) representation of the same structure picture:

The following table compares advantages and disadvantages of the two kinds of representation:

	Flat	Rendered
Lighting	Light bulbs will be used on atoms. Their position and intensity depends on light source definitions.	Uses shading for all objects (except for text). This gives atoms and bonds the best 3D impression. Several components of a light source can be defined.
Edges	Flat objects mostly have edges for a better distinguishing between objects and background.	There are no edges. The objects distinguish from each other or background because of their shading.
Shading edge, Front emphasizing	Shading edge and emphasizing of lines of front objects can be used to enhance a 3D impression.	Neither shading edge nor front emphasizing are used, since there are no edges in this kind of representation.
Pattern	Patterns may be used (e.g. ORTEP-like patterns) to enhance a 3D impression of atom balls or ellipsoids.	Patterns will not be used, since shading gives a better 3D impression.
Hatching	Hatching may be used for polyhedron faces.	Hatching is not used for polyhedron faces.
Depth cueing	Objects in the rear become darker.	Objects in the rear become darker.
Printout	Best representation on black-and-white printers.	Best representation on color printers.
Metafile/Bitmap	All graphical objects will be saved in the Windows Metafile and can be scaled in other applications. The picture can also be saved as bitmap.	3D graphical objects cannot be saved in a Windows metafile. Save a rendered representation as bitmap - at best with a higher resolution than the structure window has.


Switching Rendering On or Off

To change between flat and rendered representation, click on the [image] button in the Display toolbar. (The button is down if rendering is active.)

Instead, you can choose the Structure command from the Display menu, and change the Rendered representation of structure picture checkbox on the Rendering page of the Display Structure dialog.


Models: Overview

For the visualization of 3D chemical structures, different models are in use:

The wire model is limited to the representation of bonds, whereas atoms are only represented as terminal points of the bonds. The wire model displays only the bonds as thin lines with the colors of the bonded atoms in parts. Non-bonded atoms are displayed as dots. This model requires defined bonds, a condition that is often not fulfilled, even in inorganic compounds. It allows a very good overview on the bonding geometry and is the method of choice for molecular structures, but the space filling of a structure cannot be represented. In rendered mode, wires can be represented as sticks (tubes) instead.

In the ball-and-stick model atoms are represented as spheres and bonds are drawn as sticks or lines. This is the standard model of DIAMOND. Only in this mode, you can display ellipsoids instead of spheres as well as coordination polyhedra.

The space-filling model does not show any bonds but atoms only, where van-der-Waals radii are used so that the spheres touch or interpenetrate. This model allows a good impression of the space filling aspects of the structure, whereas constitutions and coordination relationships are difficult to recognize. The space-filling model can also be superimposed on another model.

The following illustration compares four representations of the same structure picture using wire (upper left), sticks (lower left), ball-and-stick (upper right), and space-filling model (lower right):

Reference:

Name

biphenyl-2-carboxylic acid

Author(s)

Dobson, Allison J., Gerkin, Roger E.

Title

Biphenyl-2-carboxylic Acid: a Layered Structure

Journal

Acta Cryst. (1998). C54, 795 - 798


Ball-and-Stick Model (Regular Model)

The ball-and-stick model is the standard model of Diamond. Only this model can represent atoms as thermal ellipsoids instead of spheres as well as coordination polyhedra.

To activate the ball-and-stick model, click on the [image] button in the Display toolbar, or choose the Structure command from the Display menu, and check the radio button Ball-and-stick on the Standard page of the Display Structure dialog.


Wire Model

The wire model is limited to the representation of bonds, whereas atoms are only represented as terminal points of the bonds. The wire model displays only the bonds as thin lines with the colors of the bonded atoms in parts. Non-bonded atoms are displayed as dots. This model requires defined bonds, a condition that is often not fulfilled, even in inorganic compounds. It allows a very good overview on the bonding geometry and is the method of choice for molecular structures, but the space filling of a structure cannot be represented.

To activate the wire model, click on the [image] button in the Display toolbar, or choose the Structure command from the Display menu, and check the radio button Wires on the Standard page of the Display Structure dialog.


Using Sticks Instead of Thin Wires

When using rendered representation, wires can be displayed as sticks (or tubes) instead. These sticks have the colors of the bonded atoms in parts and are rounded at the terminal points.

To enable the sticks representation in the rendered wire model, choose the Structure command from the Display menu, which opens the Display Structure dialog. From the Rendering page, check the radio button Sticks, and define a radius (in Angstroems) that will be used for all sticks globally.


Space-Filling Model

The space-filling model does not show any bonds but atoms only, where van-der-Waals radii are used so that the spheres touch or interpenetrate. This model allows a good impression of the space filling aspects of the structure, whereas constitutions and coordination relationships are difficult to recognize.

To activate the wire model, click on the [image] button in the Display toolbar, or choose the Structure command from the Display menu, and check the radio button Space-filling on the Standard page of the Display Structure dialog.

To edit the radii, see the article "Designing Atoms and Atom Types: Radii".


Superimposition of Space-Filling Model

You may draw a space-filling model over the regular wire or ball-and-stick model. Normally transparency will be used for this overlaid model.

To change the settings for a superimposition of a space-filling model, choose the Structure command from the Display menu, which opens the Display Structure dialog. From the Rendering page, choose one of the settings described below:

No superimposing	No additional space-filling-model will be drawn over the regular wire or ball-and-stick model.
Transparent	An additional space-filling-model will be drawn over the regular wire or ball-and-stick model with transparent spheres. The transparency is given in Factor, which has a range of 0 to 1. With a factor of zero, the space-filling model keeps invisible, with 1 it is opaque (not transparent).
Opaque	The additional space-filling model will be drawn with non-transparent spheres.

Usually you will check the Transparent radio button to get the superimposing model translucent and use a factor of about 0.2 to 0.5 (default).

The following picture shows two molecules of biphenyl-2-carboxylic acid in the ball-and-stick model with a superimposed space-filling model having a transparency of 0.2.

Reference:

Name

biphenyl-2-carboxylic acid

Author(s)

Dobson, Allison J., Gerkin, Roger E.

Title

Biphenyl-2-carboxylic Acid: a Layered Structure

Journal

Acta Cryst. (1998). C54, 795 - 798


Double Buffering: Overview

Double buffering is a technique, where all drawings are first written into memory (into a so-called "bitmap"), and then copied fast into the structure window (screen buffer). This technique offers flicker-free display, especially when the structure is rotated or shifted in the window.

To enable or disable double buffering, choose the Options command from the Tools menu, which opens the Options dialog. On the Desktop page, activate or deactivate, rsp., the checkbox Double buffering.

Some technical remarks about double buffering in Diamond

Double buffering works slightly different in flat and rendered representation:

In flat representation, Diamond stores the contents of the structure picture in a bitmap that has the dimensions of the full screen. Thus a picture need not be redrawn, if a structure window is being resized. Instead Diamond copies the bitmap centered into the structure window. If for example the screen has a resolution of 1024 x 768 pixels, and the client area of the structure window (that means the window except border, title bar, etc.) has a resolution of 600 x 400 pixels only, 212 pixels will be cut on both the left and right side of the bitmap as well as 184 pixels on both the upper and lower side, when it is copied into the window.

In rendered representation the bitmap has actually the size of the structure window's client area, which means it must be redrawn if the structure window is being resized.

If a structure window is in part or completely hidden by another application's window, it must be redrawn after that window is removed. This works quickly for both flat and rendered representation, because only the bitmap is copied into the structure window without calling the drawing function.

In flat mode, double buffering does not work if page mode has been activated, but in rendered mode it does.

Please note that the bitmaps used for double buffering may occupy a lot of your computer's memory. A bitmap with a resolution of 1024 x 768 pixels and 24 bit colors ("True Color") needs about 2,359,296 bytes of memory. When you have opened multiple structure windows, this amount will be occupied for every window.


Page View: Overview

In page view mode, you can see the entire page that will be sent to the printer, if you print out the current structure picture. The article "Page View vs. Normal View" will describe how to switch between page view and normal mode and the limitations of the page view mode.

The difference between page view mode and print preview mode is describe in the article "Page View vs. Print Preview".

A grid may be useful for the positioning of objects like text etc., to estimate the size of the structure window or printout page or to find the position of the current center of rotation in the structure picture.


Page View vs. Normal View

To switch between normal mode and page view mode, press the [image] button in the Display toolbar. If page view mode is active, the button is down.

The following table shows differences between normal and page view mode:

	Normal mode	Page view mode
Background color	Uses the defined background color or is white if black-on-white mode has been activated.	Is white in any case.
Auto color	The color "Auto" is black if black-on-white mode is active, otherwise white.	The color "Auto" is black in any case.
Page format	The page format is ignored.	The page format comes from the current printer settings, which can be checked or changed with the Print setup command in the File menu.
Scaling	The enlargement factor is used to scale the structure's dimensions from Angstroems to centimeters.	The structure is stretched so that the entire page fits into the structure window.
(Auto)-Adjust	The structure is fitted to the current size of the structure window.	The structure is fitted to the current size of the printing page.
Double buffering	Works for both flat and rendered representation.	Does not work unless rendered representation is used.


Page View vs. Print Preview

Print preview is a standard implementation in many MS Windows application that reproduces the printout on the screen. The following table shows the differences between page view and print preview mode:

	Page view mode	Print preview mode
Double buffering	Works if rendered representation is used.	Never uses double buffering.
Zooming	The page is fitted automatically to the structure window size.	The page can be zoomed in three steps.
Editing	The structure can be edited like in normal mode (selecting objects, rotating, etc.).	The structure cannot be edited.

To enter print preview mode, choose the Print preview command from the File menu, or press the [image] button in the standard toolbar.


Grid

Diamond can display a grid in the normal as well as in page view mode, which may be helpful for the positioning of objects like text etc., to estimate the size of the structure window or printout page or to find the position of the current center of rotation in the structure picture. The grid appears only on the screen and will never be printed or written to a metafile.

To enable or disable the display of the grid, push the [image] button in the Display toolbar. To change further settings, choose the Grid command from the Display menu, which opens the Grid dialog.

Defining the unit

In the Unit group, you can define the unit as well as the distance between the lines of the grid. Possible units are Angstroem and centimeters. The corresponding distance values are defined in the Delta input fields. The distance depends on the current enlargement factor if defined in Angstroem. If central projection is used, this is the distance for z = 0, that means on the z level of the rotational center (with z refering to the view coordinate system).

Defining the origin

The Origin group defines the origin of the coordinate system of the grid. In all cases the scale points to the right and up.

Left bottom	The origin is in the lower left corner of the structure window or the page, if page view mode is active.
Window center	The origin is in the center of the structure window or the page, if page view mode is active.
View Coordinate's System origin	The origin is identical with the projection of the center of the rotation in the structure window or on the page. Thus the grid origin moves with the center of rotation, if the structure is shifted.


Projection: Overview

This chapter will tell you how Diamond projects the structure from the Angstroem-sized real world into the structure picture.

•	Diamond uses two kinds of projection: parallel and central projection ("perspective").

•	The enlargement factor is used to transform the Angstroem 3D view coordinates into centimeter coordinates.

•	The structure picture can be adjusted to fit in the structure window.

•	The viewing distance is used for central projection and defines the perspective impression.

•	"Distortion of Atoms and Bonds" gives some workarounds to avoid distortions of atoms in central projection.

•	Both enlargement factor and viewing distance can be changed with the mouse or with the keyboard.

•	A rectangular area of the structure window can be zoomed.

•	The last article of this chapter tells you how to use stereo representation.


Parallel and Central Projection

To display the objects (atoms, bonds, etc.) of the structure on the two-dimensional area of the picture (screen or printout) the view coordinates of the objects must be converted from the three-dimensional world with Angstroem units to a two-dimensional coordinate system with centimeter units. There are two different methods to consider the z-coordinate, that means the depth, of the objects:

•	Parallel projection simply ignores the z-coordinates of the objects and uses the enlargement factor only to convert the Angstroem units of the objects to centimeter units on the picture.

•	Central projection regards the z-coordinates relative to the position of the viewer. This position is indirectly defined by both enlargement factor and viewing distance (in centimeters). Objects in the rear become smaller, whereas objects in the front become bigger than in parallel projection.

For both projection methods, the current center of rotation is an important reference point. This point will be placed into the center of the picture (screen or printout). But you can shift the projection of this reference point within the picture (see "Orientation and Position").

To change between parallel and central projection:

•	Choose the Structure command from the Display menu, which opens the Display Structure dialog. On the Standard page of this dialog, check the parallel radio button for parallel projection, or the central radio button for central projection;

•	or: use the "hotkey" Shift+Ctrl+P;

•	or: push the [image] button in the Display toolbar.

The following illustration compares two layers in graphite to show extreme perspective effects. The parallel projection in the upper and the central projection in the lower half (viewing distance: 25 centimeters, enlargement factor: 0.8 centimeters per Angstroem):


Enlargement Factor

The enlargement factor is used to transform the view coordinates of the objects from Angstroem units to the two-dimensional centimeter units of the picture (screen or printout).

In parallel projection, this value is used to transform the x- and y-coordinates of the objects, while the z-coordinate (the depth) is ignored.

If central projection is used instead, the enlargement factor refers to the z-position of the current center of rotation, whereas objects nearer than the center are represented bigger, but those behind smaller. The perspective effect depends on the current viewing distance.

To edit the enlargement factor, choose the Structure command from the Display menu, which opens the Display Structure dialog. On the Standard page of this dialog, edit the input field Enlargement factor.

You can also change the enlargement factor incrementally using the keyboard or the mouse.


Adjusting the Structure

You can adjust the structure picture to the current size of the structure window or the size of the page, if Diamond is in page view mode (see "Page View: Overview"). Adjusting can be done manually or automatically. When Diamond adjusts the structure, it changes the enlargement factor and the position of the projection of the structure within the drawing area until the picture fits into its frame, regarding a given border.

Adjusting the structure manually

To adjust the picture to the current size of its window or page, push the [image] button in the Display toolbar or use the "hotkey" Alt+F9. Adjusting can be combined with centering, which means the center of rotation is set into the center of all created atoms. For that, push the [image] button in the Display toolbar or use the "hotkey" F9.

Defining the border for adjusting

You can define a border for the adjustment procedure. The default value is one centimeter for all four borders of the window or printout page, rsp. To change the border, choose the Adjust command from the Display menu and change the values in the input fields of the Adjust dialog.

Automatic adjustment

You can make Diamond adjust the structure whenever it needs redrawing, that means whenever the structure picture changes. For that, choose the Adjust command from the Display menu and check the checkbox Automatic adjustment in the Adjust dialog.


Viewing Distance

The viewing distance defines the distance between your viewing position (or the "camera" position) and the drawing area or the screen, rsp. More exactly it is the distance between the current center of rotation of the structure and the viewers' position on the z-axis of the view coordinate system. The distance is given in centimeters (cm). The perspective impression is the stronger the lower this distance is set. Additionally a big enlargement factor contributes to this impression, because the distance is defined in cm and thus depends on the enlargement factor. In extreme cases, i.e. if objects are positioned on a level with the viewer or even behind him, the drawing of these objects will be suppressed.

To edit the viewing distance, choose the Structure command from the Display menu, which opens the Display Structure dialog. On the Standard page of this dialog, edit the input field Camera distance. Assure that the central radio button is checked, since the viewing distance takes no effect in parallel projection.

You can also change the viewing distance incrementally using the keyboard or the mouse.


Distortion of Atoms and Bonds

When using central projection, objects (especially atom spheres or ellipsoids) are distorted. That means, spheres become "eggs" in extreme cases (big enlargement factor and small viewing distance).

In flat representation, Diamond does not regard this distortion for atom spheres, so that they will simply be projected as circles, whereas ellipsoids will be distorted correctly. For that reason, the piercing points of bonds may not touch the atoms correctly.

To avoid this problem, either use rendered representation, or represent the spheres as ellipsoids, as far as displacement parameters have been defined.

The following picture shows extreme distortions for a bis(triphenylphosphineiminium) molecule with an enlargement factor of 1 cm/Å and a viewing distance of 10 cm:


Changing Enlargement Factor or Viewing Distance With Mouse or Cursor

You can change both enlargement factor and viewing distance with the mouse or with the keyboard.

Using the mouse

1. Press the [image] button in the Tracking toolbar to activate the tracking mode. The mouse cursor will change to this symbol:

2. To couple the enlargement factor with the mouse position, press down the left mouse button. The mouse cursor will change to this symbol: .

3. While holding down the left mouse button, move the mouse vertically. The structure will continuously be redrawn with a varied enlargement factor.

4. To stop the continuous variation of the enlargement factor, release the left mouse button.

5. To end the tracking mode, press the [image] button in the Tracking toolbar.

To change the increment per mouse movement, choose the Options command from the Tools menu. From the Options dialog, choose the Tracking page, and edit the value in the input field Enlargement factor per cm mouse.

Using the keyboard

Push the End key to increase or the Home key to decrease the enlargement factor. To change the increments per keystroke, choose the Options command from the Tools menu. From the Options dialog, choose the Stepping page, and edit the value in the input field Enlargement factor per keystroke.


Zooming a Rectangular Area

You can zoom a rectangular area of the structure window to the current size of the window. For that, the enlargement factor will be increased and the position of the structure moved so that the rectangular area fits optimally within the structure window.

To zoom a rectangular area, push the [image] button in the Display toolbar. The mouse cursor will change to a special symbol symbolizing a dotted rectangle.) Then perform the following steps:

1. Move the mouse cursor to the upper left corner of the desired area.

2. Press the left mouse button down and move the mouse cursor (with mouse button still down!) to the lower right corner of the desired area.

3. Release the mouse button. After that the structure will be enlarged and re-positioned.


Stereo Representation

When a 3D structure is projected into two-dimensional space, usually most of the depth information gets lost. Stereo representation of the structure is a good workaround for that limitation. For that, the structure is drawn twice side-by-side, where each is rotated before around the y-axis of the view coordinate system for the stereo angle (the left picture in positive direction, the right picture in negative direction). The distance between the two stereo pictures, the stereo distance, is the distance between the two projections of the current center of rotation.

To enable or disable stereographic representation, push the [image] button in the Display toolbar. Instead, you can choose the Structure command from the Display menu. On the Standard page of the Display Structure dialog, enable or disable, rsp., the enabled checkbox in the Stereo group.

To change the stereo angle and the stereo distance, edit the input fields Stereo angle and Pictures' distance, rsp.

The default values are six degrees and ten centimeters, rsp.

Please note that for a correct stereoscopic projection a central projection is also necessary.

For the inspection of a stereo picture stereoscopic glasses should be used. Those glasses separate both pictures by a system of mirrors. With some practice, a stereo picture can also be inspected without such aid. Look between both pictures and focus to an infinite point (try to squint a little bit). Doing so a third picture, which is 3-dimensional, appears between the others.


Lighting: Overview

Diamond uses lighting effects for both flat and rendered representation, but in a quite different way. Although for both methods parallel light is used with a directional vector defining the position of the light source, the shape is quite different.

"Lighting Effects for Standard Representation" describes what parameters are used for flat representation.

"Lighting Effects for Rendered Representation" describes how to handle lighting for rendered representation.

To enable or disable lighting, push the [image] button in the Display toolbar. Or choose the Structure command from the Display menu, and then change to the Lighting page of the Display Structure dialog.


Lighting Effects for Standard Representation

If Diamond uses flat representation, the following settings are used for lighting:

•	Position of the light source, defined by a directional vector in view coordinates (e.g. the vector (0,0,1) defines light coming from the positive end of the z-axis of the view coordinate system, that means from the viewer's position).

•	A relative intensity (0 through 1) of the light.

To edit the lighting settings for flat representation, choose the Structure command from the Display menu, and then change to the Lighting page of the Display Structure dialog.

Switching light source on or off

Check the checkbox Enable lighting to enable lighting. Otherwise no lighting will be used and the controls on the Lighting page of the Display Structure dialog are not available.

Intensity of light

Define the intensity of the light with the input field Standard intensity.

With a value of 0, no lighting is used, whereas 1 leads to maximum intensity. Diamond's lighting value is an empiric value:

a) Atoms get a lighting bulb if the intensity lies between 0 and 0.5 with a color interpolated between the atom's main color (0.0) and white (0.5). For values higher than 0.5 the bulb is white too. Note: Thermal ellipsoids will never be lighted.

b) A polyhedron face appears white if the intensity is 1.0 and the light falls on it orthogonally. Faces on the opposite side of the light source appear black. For lower intensities and non-orthogonal light falls, the color is interpolated between the faces' main color and white or black, rsp.

Position of light source

The three input fields Light source vector;... define the x-, y-, and z-component of the directional vector of the light source in view coordinates. This vector points from the center of rotation towards the light source, which is infinitely far away. If the vector is set to (-1, 1, 1) e.g., the light comes from the upper left front.

The other controls on the Lighting page will be used for rendered representation only. That means you can neither define different light components nor a color composition. The light for flat representation is white in any case.


Lighting Effects for Rendered Representation

If Diamond uses rendered representation, lighting effects depend on two different groups of settings:

(1) Global settings (the light source itself):

•	Position of the light source, defined by a directional vector in view coordinates (e.g. the vector (0,0,1) defines light coming from the positive end of the z-axis of the view coordinate system, that means from the viewer's position).

•	The ambient, specular, and diffuse components, each composed by a red, green, and blue part.

(2) Individual settings (material properties of the objects):

•	For each atom, bond, and polyhedron face, the red, green, and blue components of a specular and emissive reflectivity are defined individually.

•	The "shininess".

•	The transparency.

The individual settings will be described for the atoms, bonds, and polyhedra, rsp.

To edit the global light settings for rendered representation, choose the Structure command from the Display menu, and then change to the Lighting page of the Display Structure dialog.

Switching light source on or off

Check the checkbox Enable lighting to enable lighting. Otherwise no lighting will be used and the controls on the Lighting page of the Display Structure dialog are not available.

Position of light source

The three input fields Light source vector;... define the x-, y-, and z-component of the directional vector of the light source in view coordinates. This vector points from the center of rotation towards the light source, which is infinitely far away. If the vector is set to (-1, 1, 1) e.g., the light comes from the upper left front.

The light is made up of three components:

Ambient light

This light does not come from any particular direction, because the rays of light have bounced around the scenery and become directionless. Objects are lit evenly on all parts in all directions by the ambient light component. Ambient light gives the whole scenery a basis brightness.

Diffuse light

This light comes from a particular direction but is reflected evenly off a surface. Even though the light is reflected evenly, the object surface is brighter if the light is pointed directly at the surface than if the light grazes the surface from an angle.

Specular light

This light is directional like diffuse light, but is reflected sharply and in a particular direction. A highly specular light tends to cause a bright spot on the surface it shines upon.

The shape of an object's surface (for example of an atom) derives from an interaction between the composition of the light source (which is a global setting for the whole scenery) and the object's individual surface properties. These surface properties are individually defined for each atom, bond, and polyhedron face.


Background: Overview

Diamond uses two different modes concerning the background of the structure picture:

1. Normal mode can use any background color. This color is usually dark and used to represent a structure picture on the screen. (The default background color is black.)

2. Black-on-white mode ignores the background color but uses white in any case. This is usually used to represent a structure picture for printouts.


Black-on-White Mode

In black-on-white mode, the background color is ignored and the background will be painted white instead (on the screen) or remains white (on printout). The "Auto" color will become black, while it is white in normal mode.

To activate black-on-white mode, choose the Structure command from the Display menu, which opens the Display Structure dialog. On the Standard page, check the Black-on-white mode checkbox.

Even if black-on-white mode is not active, black-on-white mode can be used for printout. (This is the default setting for Diamond.) To disable black-on-white mode for printout, choose the Options command from the Tools menu, which opens the Options dialog. On the Desktop page, clear the checkbox Print black on white. To produce a printout with background color, both black-on-white settings must be disabled.

Both page view and print preview use the same setting as for the printout, which means that the background is white by default in these modes.


Background Color

Any color can be defined for the background, but this color will be ignored, if black-on-white mode is active.

To edit the background color, choose the Structure command from the Display menu, which opens the Display Structure dialog. On the Standard page, push the Background color button. This opens the MS Windows standard color dialog, where you can select a pre-defined color or define a new color by specifying RGB (red, green, blue) or HSL (hue, saturation, lightness) values. After you have selected or defined the color, you must push the OK or Apply button in the Display Structure dialog to take the new color into affect.


Other Effects: Overview

This chapter informs about further settings that can be defined for a structure picture:

•	Depth cueing makes objects brighter or darker dependent from the object's "depth", i.e. the z-value (in view coordinates).

•	The shading edge is an edge (additionally to the edge that is mostly used for an atom or bond) around each atom and bond and is used to bring them out from other objects in the rear.

•	Front emphasizing is used to enlarge the width of the edges of atoms, bond tubes, polyhedra etc. This value is added to the generic width of the edges. The front emphasizing value refers to the most front object of the picture and is interpolated for all objects with z > 0 between 0 and this value. The edges of objects with z < 0 leave unchanged.

•	Bond tapering distorts thick bonds, which are displayed as tubes, for a better impression of depth.

•	The overall radius factor defines a factor all atomic radii are multiplied with - but only in the ball-and-stick model.


Depth Cueing

Depth cueing is an effect that makes objects brighter or darker dependent from the object's "depth", that means the actual distance from the viewer. Normally objects in the rear become darker, but you have the possibility to reverse this effect by defining a negative value for the depth cueing intensity.

You can switch depth cueing on or off, simply by pushing the [image] button in the Display toolbar.

To enable or disable depth cueing and to define its intensity, choose the Structure command from the Display menu, which opens the Display Structure dialog. You will find the settings in the Depth cueing group.

To enable depth cueing, check the checkbox enabled.

To define the intensity of depth cueing, edit the value in the Intensity input field. The intensity is defined in RGB units per Angstroem. That means, an object is 10 units per color component (red, green, blue) darker, if its z-value of the view coordinates is 1 Angstroem smaller than an object, which is 1 Angstroem nearer. The depth values are relative to the current center of rotation, so that objects with z = 0 keep their original brightness. In rendered representation, unlike in flat representation, objects in the front will not become brighter. The range for each color component is 0 (no intensity) through 255 (maximum intensity). The depth cueing effect is the stronger the higher the absolute intensity value is. A negative sign inverts the effect, that means objects in the rear become brighter, instead of darker. Inverted depth cueing gives good result for colored printouts on white background, since the objects in the rear seem to vanish in the haze.


Shading Edge

Shading edges can be drawn around atoms and bonds to bring them out from other objects in the rear. This kind of edge is different from the edge that may be defined for atoms and thick bonds.

The shading edge is only used in flat representation.

To edit the line thickness of the shading edge, choose the Structure command from the Display menu, which opens the Display Structure dialog. On the Standard page, edit the value in the input field Shading edge. If you do not want any shading edges, enter a value of zero. Otherwise enter the line thickness in millimeters.

The use of shading edges decreases the drawing speed, since shading edges and their associated objects must be drawn separately. The shading edge will only "separate" objects from those in the rear but not be used for interpenetrating atoms and bonds. That means there is no shading edge between an atom and bonds leaving the atom into the viewer's direction. The following picture will illustrate the usage of shading edges (here it has a thickness of 1 millimeter):

Reference:

Name

Bis(triphenylphosphineiminium) 15-carbonylpentaosmium carbide iodide

Formula

(((C6 H5)3 P)2 N) (OS5 C (C O)15 I)

Author(s)

Jackson P F, Johnson B F G, Lewis J, Nicholls J N, McPartlin M, Nelson W J H

Title

Synthesis of the Carbido Anion (Os5 C (C O)15 I)and the X-Ray Crystal Structures of Os5 C (C O)15 and Ph3 P)2 N) (Os5 C (C O)15 I)

Journal

JCCCA 1980 (1980), pp. 564 - 566


Front Emphasizing

Front emphasizing means that the edges of atoms, bond tubes, polyhedra etc. in the front are thicker than those in the central or rear part of the structure picture. This is the method of choice if you want to enhance the 3D impression on a pure black-and-white printout, where you cannot use depth cueing.

Since there are no edges in rendered representation, front emphasizing is only used for flat representation.

Diamond uses a value which is added to the generic width of the edges in the front. The front emphasizing value refers to the most front object of the picture and is interpolated for all objects with z > 0 between 0 and this value. The edges of objects with z < 0 leave unchanged.

To edit the front emphasizing value, choose the Structure command from the Display menu, which opens the Display Structure dialog. On the Standard page, edit the value in the input field Front emphasizing. The value has the dimension millimeter.

The following picture shows the effect of front emphasizing for two layers of graphite:


Bond Tapering

Bond tapering is an effect that distorts thick bonds from tubes to tapers or cones to enhance the 3D impression of the structure picture. The front end of each bond has the thicker end of the taper, the rear end has the thin end or - in extreme cases - the peak of the cone.

Bond tapering is used for both flat and rendered representation.

To edit the bond tapering factor, choose the Structure command from the Display menu, which opens the Display Structure dialog. On the Standard page, edit the value in the input field Bond tapering factor. For a value greater than 0, cylindric tubes are distorted to tapers with the thicker end in the front. In the extreme case, i.e. the tube is parallel to the z-axis and the bond tapering factor is 1 (or higher), the taper becomes a cone. Tapering factors higher than 1 may be used to distort even bonds at acute angles to the drawing area to cones. Negative values would invert the effect, leading to thicker ends in the rear and thin ends in the front.

The following illustration displays a molecule of [1,2-Di(methoxyethyl)cyclopentadienyl]-trichlorozirconium(IV), in the left half with a bond tapering factor of zero, in the right half with a factor of one.


Overall Radius Factor

The overall radius factor is used as a general multiplier for atoms to be displayed in the ball-and-stick model. This value is one by default, but can be changed to increase (> 1) or decrease (< 1) the radii of the atoms globally.

The overall radius factor works only in ball-and-stick model. It does not take effect in space-filling model.

To edit the overall radius factor, choose the Structure command from the Display menu, which opens the Display Structure dialog. On the Standard page, edit the value in the input field Overall radius factor.


Designing Atoms and Atom Types: Overview

Diamond associates designs, radii, and other properties to each atom type. When atoms are created, each new atom will get the properties of the corresponding atom type. To get more information about "created" atoms and atom types, see the article "About Atoms, Atom Types, Bonds, and Bond Types: Overview". The properties of every single created atom can be changed afterwards independent from its associated atom type.

The articles of this chapter describe:

•	How to edit design, radii, and other properties for the atom types of the current structure.

•	How to edit design, radii, and other properties for individual atoms.

•	How to design colors and styles (interior, edge, pattern) of an atom type design or atom design.

•	How to edit the radii of the atom types or created atoms.

•	How to define material properties for rendered representation.

•	How to assign selected properties to all atom types of the current structure.

•	How to copy the style of an atom and paste it to selected atoms.


Designing Atom Types

The design, radii, and other properties of each atom type serves as basis for all created atoms associated with that atom type. When you alter the properties of one or more atom types, these changes may overwrite the properties of all created atoms associated with those atom types.

To open the Atom Types dialog, choose the Atom types command from the Edit menu. The dialog offers four pages:

•	Definition: Defines symbol, a short description (optional) of an atom type, and lets you assign atoms of the parameter list to the selected atom type. Compare "Atom Types" and "Assigning a New Atom Type at Runtime".

•	Design: Defines style, interior, edge, and pattern properties.

•	Radii: Defines several radii used for drawing or for calculating bonding spheres.

•	Material: Defines surface properties of an atom type for rendered representation.

The Definition page of the Atom Types dialog

Select the atom type you want to edit from the list at the upper left of the dialog box, and make the changes on the several pages of the dialog as far as needed. You will find details about colors, styles, radii, etc. in the following articles:

- Colors and Styles,

- Radii,

- Material Properties.

Updating existing atoms

By default, Diamond updates all created atoms when you close the Atom Types dialog with OK. That means each created atom gets the design of its associated atom type. If you define red oxygen and black carbon atom types, for example, all oxygen and carbon atoms in the structure picture become red and black, rsp. Individual settings will be overwritten. To disable this automatic update mechanism, switch off the Update atoms checkbox.

The disabled update mechanism may be useful for the following situation:

You have filled the contents of the unit cell, with e.g. all oxygen atoms red. Now you want to display further coordination spheres with oxygen atom yellow. Then you do the following steps:

1. Define the color red for the atom type O.

2. Fill the contents of the unit cell.

3. Define the color yellow for the atom type O. Assure that the Update atoms checkbox is not checked.

4. Continue building up the structure, for example fill the coordination spheres.

Updating resources

The Diamond configuration file contains design informations for some hundreds of atom types. If the checkbox Update resources is checked, these informations will be updated whenever you confirm the Atom Types dialog with OK.

Resetting all atom type designs

If you want to reset all colors, styles, radii, etc. for all atom types of the current structure, push the Reset all button. This will overwrite all settings with those from the Diamond configuration file.


Designing Selected Atoms

This article describes how to edit the colors, styles, radii, and material properties of a single atom or of multiple selected atoms. These settings are defined in the Edit Atom(s) dialog, which uses three pages:

- Design: Defines the colors and styles of the atom(s).

- Radii: Defines the drawing radii of the atom(s).

- Material: Defines surface properties of the atom(s) for rendered representation.

Editing a single atom's properties

The easiest way to design a single atom is to double-click on the atom. Instead, you can click with the right mouse button on the atom, and then choose the Edit atom(s) command from the context menu.

Editing properties for multiple atoms

Select the atoms you want to edit. There are several ways to select atoms; see the article "Selecting Objects". Then click with the right mouse button into one of the selected atoms, and choose the Edit atom(s) command from the context menu.

Properties which are not unique for all selected atoms, keep blank in the corresponding control in the dialog box. For example, if you have selected nine atoms with the interior color red and one with yellow, the color selection field for the interior color will be empty. If you leave this field empty, the interior colors of the selected objects will be untouched. If you select a color, all selected atoms will get that new interior color.

In this screenshot a complete molecule has been selected. Since the selected atoms use different styles and interior colors, the fields Style and Interior color are blank, whereas the other settings are unique.


Colors and Styles

The design of an atom or atom type is made up of the following settings:

Style	Defines if and what pattern is used for the atom, or if the atom is invisible.
Interior color	Defines the color that is used to fill the interior of the atom.
Interior brush	Offers several options for the interior, like hatching, transparency, etc.
Edge color	Defines the color that is used to draw the edge of the atom.
Edge pen	Offers several options for the edge, like a dotted edge or no edge.
Edge thickness	Defines the line thickness for the edge.
Pattern color	Defines the color that is used to draw the pattern, as far as selected.
Pattern thickness	Defines the line thickness for the pattern.

Since rendered representation uses neither edges nor patterns or hatching, some of the above settings will be used only in flat representation.

You will find all these settings on the Design page of the Edit Atom(s) dialog or Atom Types dialog, rsp.

Styles

Diamond offers several styles, most of them are ORTEP-like. If simple spheres are used to display atoms (non-ellipsoid representation), Diamond uses pre-defined patterns, which means that the axes and ellipses in the pattern do not represent any directions of thermal vibrations. In ellipsoid representation, the axes and ellipses will of course be calculated correctly. The following illustration lists all available styles in spheroid (upper row) and ellipsoid representation, rsp.

From the left to the right: Solid/Empty, Cross 1, Cross 2, Octand, Shadow, Crescent

The last "style" in the style list is "invisible". This style is used to display broken-off bonds.

Interior color and brush

Defines if and how the atom is filled and which color is used, as far as necessary. The color is defined in a color select box. Several brushes are available to fill the interior:

Solid	The default setting. The interior is filled opaque with the interior color.
Transparent	The interior of the atom is not filled. Thus objects behind the atom will shine through the atom.
Background	The interior color is ignored, and the background color is used instead.
Hatching 1, 2,...	The interior is filled opaque with the interior color, and a hatching is used with the pattern color. Hatching can be used together with all styles, but this looks rather horrible. Please note that standard MS Windows hatching brushes are used for this option, which depends on the resolution of the output device. That means the density of lines is much more higher on a 600 dpi printer than on the screen (about 100 dpi).

The six hatching types used by Diamond.

Edge color, pen, and thickness

Defines if and how an edge is drawn around an atom and which color is used, as far as necessary. Several pens are available for the edge:

Solid	The default setting. The edge is drawn as solid line with the edge color and the given thickness in millimeters.
Dash	The edge is drawn as dashed line with the edge color, whereas the thickness is ignored.
Dot	The edge is drawn as dotted line with the edge color, whereas the thickness is ignored.
No edge	Draws no edge.
Background	Draws the edge solid, but ignores the edge color and uses the background color instead.

Pattern color and thickness

Defines the color and the line thickness in millimeters for a pattern if the atom style uses a pattern. The color is also used for a hatching brush (see Interior settings).

Invisible edges and/or interior

If you assign the style "invisible" to an atom, this will not be drawn, and all bonds to that atom will be shortened ("broken-off" bonds). If you want to avoid the broken-off effect, you should use the style "Solid/Empty" instead, together with a transparent brush and "No edge".

Rendered representation

When using rendered representation, atoms use the interior color only. No edge and no pattern or hatching is used.


Radii

For each atom or atom type, two different drawing radii can be defined, the radius for ball-and-stick and the radius for space-filling model.

For atom types (but not for single atoms), you can also define the effective radius, which is used to calculate bonding spheres.

You can edit the radii on the Radii page of the Edit Atom(s) dialog or Atom Types dialog, rsp.

Drawing radius for ball-and-stick model

Defines the radius in Angstroems which is used to display the atom or an atom basing upon this atom type in the ball-and-stick model. This radius may be multiplied with several additional factors:

(a) The "overall radius factor", which is used to enlarge or decrease all atoms in the same way, and which is usually 1.0.

(b) The "ligand atoms reducing factor", which is used to decrease the size of atoms on corners of coordination polyhedra.

Drawing radius for space-filling model

Defines the radius in Angstroems which is used to display the atom or an atom basing upon this atom type in the space-filling model.

Effective radius (for bonding spheres)

The effective radius is used only by atom types and is defined in Angstroems like the drawing radii. This radius is used to calculate bonding spheres. For more information, how bonding spheres are calculated, read the article "Bond Types".


Material Properties (Atoms)
Material Properties

For each atom type or atom, individual material properties (surface properties) can be defined. These properties define the shape (shining or matt) of the atom in rendered representation, whereas they take no effect in flat representation.

You can edit the material properties on the Material page of the Edit Atom(s) dialog or Atom Types dialog, rsp.

The material properties consist of:

Specular reflectivity	Defines the red, green, and blue component of the atom's reflective properties for the specular component of the light source. A high specular reflectivity leads to a shiny atom, since it reflects specular light very well. The intensity of the specular highlight on the atom depends further on the intensity of the specular component of the light source. Using different red, green, and blue components leads to a colored highlight (instead of white highlight).
Emissive reflectivity	Defines the red, green, and blue component of the emissive properties. These components are usually zero. Values greater than zero let the atom behave as indirect light source, which means it reflects specific components of the direct light source. Different values for the components red, green, and blue "falsify" the original color of the atom, which is defined by the interior color.
Shininess	This property sets the specular exponent of the material, which specifies how small and focused the specular highlight is. A value of zero specifies an unfocused specular highlight, which is actually what is producing the brightening of the colors evenly across the entire polygon. (The atom sphere is made up of a mesh of polygons.) If you set a value of 1 through 128, you reduce the size and increase the focus of the specular highlight, causing a shiny spot to appear. The larger the value, the more shiny and pronounced the surface. The default value is the maximum value of 128.
Transparency	Defines the transparency of the atom. A value of zero (which is the default) means that the atom is opaque. The maximum value of one makes the atom completely transparent, that means invisible.

Material properties interact with the components of the light source. If you use for example red specular light (green and blue specular component set to zero), the specular highlight appears red instead of white, if you use specular reflectivity of Red=1, Green=1, and Blue=1. If you use different components for specular reflectivity instead, the color changes due to interaction between light source and what the surface reflects and absorbes.

The following illustration compares nine different material settings for an atom with the interior color red, and the following light properties (default settings):

- Specular: Red = Green = Blue = 1

- Diffuse: Red = Green = Blue = 0.8

- Ambient: Red = Green = Blue = 0.3

First row: All atoms with specular reflectivity Red = Green = Blue = 0.

Left: Emissive reflectivity Red = Green = Blue = 0.

Middle: Emissive reflectivity Red = 1, Green = Blue = 0.

Right: Emissive reflectivity Red = Green = Blue = 1.

Second row: Variation of shininess. All atoms with specular reflectivity Red = Green = Blue = 1 and emissive reflectivity Red = Green = Blue = 0.

Left: Shininess = 1

Middle: Shininess = 10

Right: Shininess = 128 (maximum and default value)

Third row: Variation of transparency. All atoms with specular reflectivity Red = Green = Blue = 1 and emissive reflectivity Red = Green = Blue = 0 and shininess of 128.

Left: Transparency = 0.25

Middle: Transparency = 0.5

Right: Transparency = 0.75.


Assigning Selected Properties to All Atom Types

When you edit the atom type designs, there is often the need to overwrite several properties of all atom types with the same value. For example, if you want to have all atom types with the same ORTEP-like pattern instead of the default style that uses no pattern, you could - one atom type after the other - select the atom type, change the style, then select the next atom type, change the style, etc.

To avoid this boring procedure, Diamond offers a dialog box where you can define, which properties all atom type design shall be overwritten by the settings of the currently selected atom type.

To assign selected properties to all atom types, follow these steps:

1. From the Edit menu, choose the Atom types command to open the Atom Types dialog.

2. In the Atom Types dialog, choose the Design page. Set the properties, which you want to assign to all other atom types, for the currently selected atom type.

3. Push the Unify button.

4. In the Unify Atom Designs dialog, activate all properties that shall be overwritten, and deactivate all properties which shall be left unchanged. (In the example above you would activate "Style" only.)

5. Press the OK button, which returns to the Atom Types dialog.

6. If you need not make further changes, confirm with OK.


Copying and Pasting Atom Styles

Diamond offers a poweful and easy to use way to assign a style to one or more selected atoms:

1. With the right mouse button, click on the atom whose style (colors, pattern, edge, radii, material properties) you want to assign to other atoms, and choose the Copy Style command from the context menu.

2. Select the atom or multiple atoms you want to assign that design to. With the right mouse button, click into one of the selected atoms, and choose the Paste Style command from the context menu.

Please note that for the Copy Style command one (and not more) atom must be selected.


Designing Bonds and Bond Types: Overview

Like for atom types, Diamond associates designs, radii, and other properties to each bond type, that means for each atom type combination. When bonds are created, each new bond will get the properties of the corresponding bond type. To get more information about "created" bonds and bond types, see the article "About Atoms, Atom Types, Bonds, and Bond Types: Overview". The properties of every single created bond can be changed afterwards independent from its associated bond type.

The articles of this chapter describe:

•	How to edit design, radii, and other properties for the bond types of the current structure.

•	How to edit design, radii, and other properties for individual bonds.

•	About the difference between thin and thick bonds.

•	About fragmentated bonds.

•	How to design colors and styles (interior and edge) of a bond type design or bond design.

•	How to define material properties for rendered representation.

•	How to assign selected properties to all bond types of the current structure.

•	How to copy the style of a bond and paste it to selected bonds.


Designing Bond Types

Like with atom types and created atoms, the design, radius, and other properties of each bond type serves as basis for all created bonds associated with that bond type. That means you can assign properties to bonds according to the atom types involved. When you alter the properties of one or more bond types, these changes may overwrite the properties of all created bonds associated with those bond types.

To open the Bond Types dialog, choose the Bond types command from the Edit menu. The dialog offers three pages:

•	Definition: Defines a short description (optional) of a bond type, and the bonding sphere. Compare "Bond Types" and "Connectivity".

•	Design: Defines style, interior, edge, and radius properties.

•	Material: Defines surface properties of a bond type for rendered representation.

The Definition page of the Bond Types dialog

Select the bond type you want to edit from the list at the upper left of the dialog box, and make the changes on the several pages of the dialog as far as needed. You will find details about colors, styles, radius, etc. in the following articles:

- Colors and Styles,

- Material Properties.

Updating existing bonds

By default, Diamond updates all created bonds when you close the Bond Types dialog with OK. That means each created bond gets the design of its associated bond type, like it is done with atom types and created atoms. To disable this automatic update mechanism, switch off the Update bonds checkbox.

Defining a default bond style

While designs can be stored for every atom type in the Diamond configuration file, bond type designs cannot. Instead, Diamond accesses a default bond design when creating new bond types. You can overwrite the default design with the current design by pushing the Save as default button in the Bond Types dialog.

Resetting all bond type designs

If you want to reset all colors, styles, radii, etc. for all bond types of the current structure, push the Reset all button. This will overwrite all settings with the default bond style.


Designing Selected Bonds

This article describes how to edit the colors, style, radius, and material properties of a single bond or of multiple selected bonds. These settings are defined in the Edit Bond(s) dialog, which uses two pages:

- Design: Defines the colors, style and radius of the bond(s).

- Material: Defines surface properties of the bond(s) for rendered representation.

Editing a single bond's properties

The easiest way to design a single bond is to double-click on the bond. Instead, you can click with the right mouse button on the bond, and then choose the Edit bond(s) command from the context menu.

Editing properties for multiple bonds

Select the bonds you want to edit. There are several ways to select bonds; see the article "Selecting Objects". Then click with the right mouse button into one of the selected bonds, and choose the Edit bond(s) command from the context menu.

Properties which are not unique for all selected bonds, keep blank in the corresponding control in the dialog box. For example, if you have selected nine bonds with the interior color red and one with yellow, the color selection field for the interior color will be empty. If you leave this field empty, the interior colors of the selected objects will be untouched. If you select a color, all selected bonds will get that new interior color.


Thin vs. Thick Bonds

While there are a lot of styles with different ORTEP-like patterns for atoms, bonds can have two different styles only: Thin and thick. Besides this, you can further assign the style "invisible".

Thin bonds are displayed as lines only. These lines can have a dotted style instead of the default solid line style and a defined thickness in millimeters to enhance them in the structure picture. In rendered representation, these thin bonds are also represented as lines only instead of 3D objects (cylinders), and will thus not be shaded.

Thick bonds are displayed as 3D objects, that means as cylinder, which may be distorted due to perspective transformation or a 3D effect, called bond tapering. In extereme cases these cylinders become cones. The radius of the bond is given in Angstroems units. In rendered representation, thick bonds are displayed as 3D objects and can be shaded like atoms.


Fragmentated Bonds

If you cut a bond into pieces each with the same length and with voids between having the same size, you get what Diamond (and at least SCHAKAL) calls a "fragmentated" bond. Fragmentation can be applied to both thin and thick bonds.

To define a bond as fragmentated and define the number of voids between the fragments, choose the Bond types command from the Edit menu, and select the Design page on the Bond Types dialog. Edit the number of voids in the input field Fragmentation. A number of zero defines a "normal" bond without fragmentation.

Several bond styles in flat (left) and rendered (right) representation: Thin bonds (in the rear), thick bonds with a radius of 0.04 Angstroems appearing as tapers (bond tapering factor of 0.8) (in the front), a thin fragmentated bond (going to the bottom atom), and a thick fragmentated bond (going to the top atom), both with a fragmentation of 4.


Colors and Styles

The design of a bond or bond type is made up of the following settings:

Style	Selects between thin, thick, and invisible.
Radius	Defines the radius of the bond in Angstroems, if it is a thick bond. This value does not effect thin bonds.
Fragmentation	Defines the degree of fragmentation of the bond.
Interior color	Defines the color that is used to fill the interior of a thick bond or the line color for a thin bond.
Interior brush	Offers several options for the interior, like hatching, transparency, etc., for a thick bond (not used for thin bonds).
Edge color	Defines the color that is used to draw the edge of a thick bond (not used for thin bonds).
Edge pen	Offers several options for the edge of a thick bond or the line of a thin bond, like a dotted edge/line or no edge.
Edge thickness	Defines the line thickness for the edge of a thick bond or the line thickness of a thin bond.

Since rendered representation uses no edges, the settings edge color, pen, and thickness will be used only in flat representation.

You will find all these settings on the Design page of the Edit Bond(s) dialog or Bond Types dialog, rsp.

Interior color and brush; Edge color, pen, and thickness

Interior color and brush as well as edge color, pen, and thickness of a thick bond works in principal like for atoms, so please compare with "Colors and Styles". For a thin bond, the interior color is used to define the line color, whereas the line style (solid, dotted, etc.) and thickness are defined by the edge pen and thickness.

Rendered representation

When using rendered representation, bonds use the interior color only. No edge is used.


Material Properties (Bonds)
Material Properties

A bond uses the same material properties as an atom, as far as it has been defined as thick bond, and rendered representation has been enabled. Then it is drawn as a real 3D object (a cylinder that may be distorted to a taper) and thus can be shaded. If it has been defined as thin bond only, it will be drawn as a simple line instead without shading effects.

For the different material properties, see the article "Material Properties".


Assigning Selected Properties to All Bond Types

Suppose all your bond types use thin green bonds, and now you want to assign all bond types thick yellow bonds with black edge, you could - one bond type after the other - select the bond type, change style and colors, then select the next bond type, change style and colors, etc.

To avoid this boring procedure, Diamond offers a dialog box where you can define, which properties of all bond type designs shall be overwritten by the settings of the currently selected bond type.

To assign selected properties to all bond types, follow these steps:

1. From the Edit menu, choose the Bond types command to open the Bond Types dialog.

2. In the Bond Types dialog, choose the Design page. Set the properties, which you want to assign to all other bond types, for the currently selected bond type.

3. Push the Unify button.

4. In the Unify Bond Designs dialog, activate all properties that shall be overwritten, and deactivate all properties which shall be left unchanged. (In the example above you would activate "Style", "Interior, color", and "Edge, color".)

5. Press the OK button, which returns to the Bond Types dialog.

6. If you need not make further changes, confirm with OK.


Copying and Pasting Bond Styles

Like for atoms, Diamond offers a poweful and easy to use way to assign a style to one or more selected bonds:

1. With the right mouse button, click on the bond whose style (colors, edge, radius, fragmentation, material properties) you want to assign to other bonds, and choose the Copy Style command from the context menu.

2. Select the bond or multiple bonds you want to assign that design to. With the right mouse button, click into one of the selected bonds, and choose the Paste Style command from the context menu.

Please note that for the Copy Style command one (and not more) bond must be selected.


Color Differentiation: Overview

Normally the created atoms use the colors of their associated atom types or the colors that you have changed later. Instead, you can use other colors to differentiate for several properties, such as formal oxidation numbers, symmetry operations, etc.

Furthermore, you have the opportunity to display the distribution of atoms on mixed sites. The article "Definition of Colors for Mixed Site Representation" describes how to define the colors for mixed site representation.


What to Differentiate For

Normally the created atoms use the colors of their associated atom types or the colors that you have changed later. Instead, you can use other colors to differentiate for several properties.

To change the color differentiation, choose the Color differentiation command from the Display menu, and select one of the following criteria (or choose the normal differentiation "Standard"):

Charges/Oxidation numbers	The colors are differentiated for (formal) oxidation states or charges. There are 13 states for the oxidation numbers -4 through +8. The charge or (formal) oxidation number is rounded to an integer.
Site occupation factors	The colors are differentiated for site occupation factors. There are 10 ranges (0.0 .. 0.1; 0.1 .. 0.2; .....; 0.9 .. 1.0) plus the differentiation for 1.0.
Symmetry operations	The number of the symmetry operation (1 through a maximum of 48, depending on the current space group) is used to differentiate.
Bravais translations	The number of the Bravais translation (1 through a maximum of 4, depending on the centering of the current space group) is used to differentiate.
Cell translations	The atoms of a cell or a cell range can be emphasized.

Example: Packing diagram of Bis(triphenylphosphineiminium) 15-carbonylpentaosmium carbide iodide with color differentiation for symmetry operations.

References:

Name

Bis(triphenylphosphineiminium) 15-carbonylpentaosmium carbide iodide

Formula

(((C6 H5)3 P)2 N) (OS5 C (C O)15 I)

Author(s)

Jackson P F, Johnson B F G, Lewis J, Nicholls J N, McPartlin M, Nelson W J H

Title

Synthesis of the Carbido Anion (Os5 C (C O)15 I)and the X-Ray Crystal Structures of Os5 C (C O)15 and Ph3 P)2 N) (Os5 C (C O)15 I)

Journal

JCCCA 1980 (1980), pp. 564 - 566

Space group	P 1 21/n 1 (no. 14)

Z	4

To change the colors for the formal oxidation numbers, symmetry operations, etc., push the corresponding button in the Edit colors group, which opens the Color Settings dialog. Select the formal oxidation number, symmetry matrix, etc. and assign it a color from the color select box.

It is recommended to display a legend of oxidation numbers, symmetry matrices, etc.


Representation of Mixed Sites

Diamond offers a method to display the distribution of atoms on a mixed site by:

1. displaying only the representative,

2. mixing the colors of all atoms on the mixed site using the ratio of the site occupation factors,

3. displaying the ratio of site occuptation as pie diagrams or as concentrical disks.

To display the distribution of atoms on mixed sites, choose the Color differentiation command from the Display menu, which opens the Color Differentiation dialog. You will find the options in the Mixed Sites Representation group.

Representative only	This is the default setting. The atom which represents the site will be drawn using its "own" design.
Mix colors	The colors of all atoms on the site will be mixed according to their relative site occupations.
Sectors	The relations of the site occupations will be represented as a kind of pie diagram.
Concentric disks	The distribution will be represented as concentric disks with radii relative to the site occupations.

The colors for multiple (trace) elements are defined with their corresponding atom types. See the article "Definition of Colors for Mixed Site Representation" how to assign these colors.


Definition of Colors for Mixed Site Representation

Up to eight colors can be defined for each atom type with mixed sites in the Atom Types dialog. To open the Atom Types dialog, choose the Atom types command from the Edit menu. If an atom type represents a mixed site, the group Colors for mixed site representation is available. Otherwise this group is hidden. The components (elements with oxidation numbers) of the mixed site are listed in the combobox Component, the corresponding colors in the color select box Color.

Example: One atom in the structure picture representing a mixed site with 60 percent Si, 30 percent Al, 8 percent Fe, and 2 percent Ni.

The default settings for the colors are those used for the atom type components. That means, if you have defined brown for the atom type "Fe+3" in the Diamond atom type resource, all Fe+3 components on mixed sites will become brown by default.


Cell Edges: Overview

This chapter tells you how to:

- add the edges of the unit cell or of an arbitrary cell range to the structure picture,

- design the cell edges,

- destroy cell edges.

Furthermore, you can switch on or off the display of the unit cell base vectors a, b, and c.


Adding Cell Edges

Cell edges can be added to the structure picture either automatically or manually. Some of the functions that build up a structure picture make use of an option, which automatically generates the cell edges within the cell range, where atoms are to be generated. The simplest case: If you generate the contents of the unit cell, the unit cell edges may be added automatically. For more informations, how cell edges can be added automatically, see the article "Filling Cell Ranges: Overview".

To add the edges of the unit cell manually, using the default design (see below), either push the [image] button in the Build toolbar, or use the "hotkey" Shift+Ctrl+E.

To add the edges of the unit cell and change the default design or add edges of an arbitrary cell range, choose the Cell edges command from the Objects menu, which opens the Cell Edges dialog. Define the six border values for the cell range (the default is XMin = YMin = ZMin = 0 and XMax = YMax = ZMax = 1, which defines the unit cell edges), adjust the style settings in the Style group, if necessary, and then push the Build button. This will generate the cell edges without closing the dialog box. Existing cell edges will not be overwritten.

The latest cell edge design will be saved as default cell edge design in the Diamond configuration file, when you close the dialog box. For more informations about cell edge design, see the article "Designing Cell Edges".


Designing Cell Edges

To change the default design for cell edges or to update the designs of existing cell edges, choose the Cell edges command from the Objects menu, which opens the Cell Edges dialog. You will find all settings in the Style group.

Select the color for the cell edges from the Color color select box, the pen from the Pen combobox, and define the thickness in millimeters in the input field Thickness. The pen can select between solid (which is the default), dotted or dashed lines. The thickness is applied only for the solid pen. Please note that the pens "dotted" and "dashed" use a MS Windows line pattern that depends on the resolution of the target device. That means the dots appear denser and the "dashes" shorter on a printer with high resolution than on the screen. If you define a thickness of zero, Diamond uses a pen that is only one pixel thick.

If you want to add new cell edges, first change the design as far as necessary in the Style group, before you push the Build button to generate the edges within the selected cell range. Please note that existing cell edges will not be overwritten. To change the style of existing cell edges, change the design, and then push the Update styles button.

Unlike (thick) bonds, cell edges cannot be displayed as cylinders, and thus not be tapered. When using rendered representation, thick cell edges will be displayed as cylinders instead of lines only, and will thus be shaded like thick bonds.

The latest cell edge design will be saved as default cell edge design in the Diamond configuration file, when you close the dialog box.


Removing Cell Edges

To delete all existing cell edges from the structure picture, choose the Cell edges command from the Objects command. In the Cell Edges dialog, push the Delete all button. This will destroy all existing cell edges, independent from the settings in the Range group. If you want to destroy only a part of the cell edges, you must first destroy all, and then re-build the desired cell edges.


Displaying the Unit Cell Axes

The three axes that define the base vectors of the unit cell, a, b, and c, can be displayed if no cell edges are displayed. To switch the display of the base vectors on or off, push the [image] button in the Display toolbar.

The axes use the color of the default cell edge design.


Thermal Ellipsoids: Overview

This chapter deals with the graphical representation of (anisotropic) displacement parameters, where atoms are displayed as ellipsoids instead of spheres only. This kind of representation leans of course heavily on the classical program ORTEP (Oak Ridge Thermal Ellipsoid Plot).

The first article describes the styles, which are available for ellipsoid representation.

"Displacement Parameters and Ellipsoid Representation" describes the relation between displacement parameters and their representation.

You can exclude selected atoms or atom types from being displayed as ellipsoid.


Thermal Ellipsoids: Styles

When Diamond draws thermal ellipsoids, it tries to reproduce the style given for the drawn atom. A lot of ORTEP-like styles is available; see "Colors and Styles" how to define the styles for atoms or atom types.

To simply switch between ellipsoid and non-ellipsoid representation, push the [image] button in the Display toolbar.

The following illustration shows the available styles, and how they are represented for a simple atom sphere or an ellipsoid:

From the left to the right: Solid/Empty, Cross 1, Cross 2, Octand, Shadow, Crescent

Thermal ellipsoids consist of the following parts:

a) the three semiaxes of the ellipsoid,

b) the border ellipse which is formed by the projection of the (threedimensional) ellipsoid onto the drawing area,

c) the three basic ellipses formed by each two of the three semiaxes of the ellipsoid. Each basic ellipse is divided into a front, visible and back, hidden part.

Diamond offers the following four styles to represent thermal ellipsoids:

1. Representation of only the border ellipse (corresponds to the ORTEP style with ORTEP instructions 704 and 714).

2. Representation of the border ellipse and the front parts of the basic ellipses (ORTEP: 702, 712).

3. Representation of the border ellipse and both front and back parts of the basic ellipses (ORTEP: 703, 713).

4. Representation of the border ellipse, the front parts of the basic ellipses, the semiaxes pointing towards you and an open, hatched octand (ORTEP: 701, 711).

The styles 2, 3, and 4 have direct pendants in the ‘normal’ ball-and-stick model. They correspond to the styles "Cross 1", "Cross 2", and "Octand" (compare illustration above). By combining style with interior, pattern, and edge color you may create empty, solid and even transparent ellipsoids. For the other styles (like "Shadow") only the border ellipse of the ellipsoid is drawn.

There are additional options for the ellipsoid representation, which you will find in the Ellipsoids dialog. To open the Ellipsoids dialog, choose the Thermal ellipsoids command from the Objects menu. Here you may select between the following additional options:

Draw basic ellipses only	If this checkbox is checked, Diamond suppresses all atom styles and draws only the three basic ellipses of each ellipsoid. The ellipsoid is not filled, i.e. it is transparent. This setting has the advantage that open ellipsoids are drawn almost as quick as normal circles, but you can still estimate the dimensions of the ellipsoid - e.g. when positioning atom labels.
Draw lines on back sides, too (Octands)	If this checkbox is checked, the program draws even the back parts of the basic ellipses if an ellipsoid is shaped with an open octand.
Solid lines on back side	If this checkbox is checked, the back parts of the basic ellipses are drawn as solid instead of interrupted lines.
Hatching (octands)	Defines how to hatch the three walls of an open octand. You may either determine the number of hatching lines for each wall (Number) or determine a fixed distance between these lines (in Angstroems, Distance). Valid values are 0 to 31 lines per wall and 0.001 to 0.25 Angstroem, rsp.

The ellipsoid probability factor (here given in percent) defines indirectly the size of the ellipsoids. The default value is 50 percent.

Atoms in ellipsoid representation may be edited individually like in ‘normal’ ball-and-stick representation. You can select an atom by clicking into the rectangle that surrounds the 2D projection of the ellipsoid.

The calculation of the border ellipse is the most time-consuming step when drawing a thermal ellipsoid. To speed up the drawing, you may activate the setting Draw border ellipses only in the dialog. But please do not forget to re-enable this setting when your picture is ready for output on printer or metafile.

Thermal ellipsoids will only be displayed with the following conditions:

1. Valid anisotropic displacement parameters must be given for at least one atom of the paramerer list.

2. The display of thermal ellipsoid must be enabled. Otherwise the atoms will be displayed as spheres only. You can simply switch between ellipsoid and non-ellipsoid representation with the [image] button in the Display toolbar. Or use the appropriate checkbox in the Ellipsoids dialog that is opened with the Thermal ellipsoids command from the Objects menu.

3. The ball-and-stick model must have been activated.

If no displacement parameters are given for an atom or if the atom is the corner of a coordination polyhedron, it cannot be represented as ellipsoid. But in general, a mixed representation of thermal ellipsoids and coordination polyhedra is possible.


Displacement Parameters and Ellipsoid Representation

Diamond works with isotropic as well as with anisotropic displacement parameters. To edit type and values of the displacement parameters, choose the Atomic parameters command from the Edit menu, which opens the Atomic Parameters dialog. The displacement parameters are defined on the Displacement page of that dialog. Compare the article "Atomic Parameters" for more information about atomic parameters and displacement parameters.

You may define one isotropic and six anisotropic displacement parameters for each single atom of the parameter list. If anisotropic parameters are given, the field for the isotropic parameter may be valid, too (e.g. after importing data from a CIF file). In this case the isotropic parameter is the equivalent displacement parameter (e.g. Ueq).

Types of displacement parameters

Diamond works with isotropic displacement parameters of the types U and B as well as with anisotropic parameters of types U, B, and beta.

a) isotropic displacement parameters

Type B:	exp (-B sin²(theta) / lambda²)

Type U:	exp (-8 pi² U sin²(theta) / lambda²)

b) anisotropic displacement parameters

Type beta:	exp ( -(h² beta11 + k² beta22 + l² beta33 + 2hk beta12 + 2hl beta13 + 2kl beta23) )

Type B:	exp ( -0,25(B11 h² (a*)² + B22 k² (b*)² + B33 l² (c*)²

+ 2 B12 hk a* b* + 2 B13 hl a* c* + 2 B23 kl b* c*) )

Typ U: 	exp ( -2 pi² (U11 h² (a*)² + U22 k² (b*)² + U33 l² (c*)²

+ 2 U12 hk a* b* + 2 U13 hl a* c* + 2 U23 kl b* c*) )

Please note that Diamond does not calculate equivalent displacement parameters from anisotropic parameters, nor does it check the relation between anisotropic parameters and a given equivalent parameter.

If for at least one atom isotropic and/or anisotropic displacement parameters are given, but no valid symbol (i.e. ? instead of U, B or beta), you will receive a warning message. When representing the thermal vibrations graphically, Diamond assumes type B which may lead to wrong results. In this case you should return to the Atomic Parameters dialog and correct the types for isotropic and/or anisotropic displacement parameters.

About the options of representing thermal ellipsoids graphically, see the article "Thermal Ellipsoids: Styles".


Exclude Selected Atom Types From Ellipsoid Representation

If anisotropic displacement parameters have not been defined for all atom types of the structure, it is often useful to exclude those atom types from being displayed as ellipsoids. In most cases, hydrogen atoms have not been refined anistropically, leading to hydrogen atoms in the structure picture, which are mostly rather big as compared with the other atom types that have been refined anisotropically.

You can define that selected atom types shall be drawn as spheres instead of ellipsoids, like in the non-ellipsoid representation of the ball-and-stick model.

To exclude an atom type from being displayed as thermal ellipsoid, choose the Atom types command from the Edit menu. In the Atom Types dialog, choose the Radii page, where you check the checkbox No ellipsoid representation.


Labelling Atoms And Bonds: Overview

This chapter deals with the use of atom and bond labels and will tell you:

- how to add labels to atoms and bonds,

- what atom and bond label texts can consist of,

- how to define the size, position, and style of the label,

- how to shift the label with the mouse,

- how to change the label text, size, position, and style of an existing label,

- how to delete atom and bond labels.


Adding Labels

There are several ways how you can add labels to atoms or bonds or to both atoms and bonds:

Labelling all selected atoms and bonds

To label all selected atoms and bonds, push the [image] button in the Build toolbar, or use the "hotkey" Shift+Ctrl+L. With this quick method, the new atom and bond labels become the latest atom label and bond label settings, rsp., or the default settings.

Labelling all selected atoms or bonds

If objects of different kinds (atoms, bonds, etc.) have been selected, but you want to label the selected atoms or bonds only, or if you want to add labels and define new settings (text, size, position, style), click into one of the selected atoms or bonds, and choose the appropriate command from the context menu, that means either the Add atom label(s) or the Add bond label(s) command, rsp. You may also choose the Atom labels command from the Objects menu. Both commands open the Add Atom Label dialog, where you can change the default or latest settings, rsp., and start the generation of labels with the OK button. If the Update existing label definitions checkbox is checked, existing labels will be overwritten using the current settings. Read the articles "Atom Label Text", "Bond Label Text", and "Style, Size, and Position" about label text, position, size, and style.


Atom Label Text

To define the text for a new atom label or to edit the contents of an existing atom label, use the controls in the Text group of the Add Atom Labels dialog box or the Edit Atom Labels dialog box, rsp. See the articles "Adding Labels" and "Changing Label Text, Style, or Size After Creation" how to add labels or how to edit existing labels, rsp.

The atom label can either have individual text or pre-defined text such as the atom symbol. Content determines the kind of information to be supplied, whereas Format decides how the information will be formatted. You may select from:

Content	Format	Description
Element symbol	Fe	Formats the element symbol: First letter uppercase, second (if defined) lowercase.
	FE	Both letters (as far as defined) uppercase.
Atom symbol	Fe 1	Formats the atom symbol without any change.
	Fe1	Formats the atom symbol, but removes blanks, e.g. blanks between an element symbol and additional identifiers.
	Fe^1^	Formats the atom symbol with the non-element part of the symbol as far as possible as superscript.
	Fe~1~	dito, but as subscript.
Atom identifier	AXYZSSB	Formats the atom code.
	PARM #	Formats the sequential number of the atom in the parameter list (beginning with #1).
	ATOM #	Formats the sequential number of the atom in the list of created atoms (beginning with #1).
Element/Charge	Fe+2	Displays the element symbol plus charge or (formal) oxidation number. Charge is added to the element symbol directly as integer with sign (even if positive).
	Fe(+2)	The integer charge following the element symbol is enclosed in parentheses.
	Fe+2.345	Charge is added to the element symbol without rounding.
	Fe(+2.345)	The charge is enclosed in parentheses and not rounded.
	Fe^+2^	Like Fe+2, but with charge as superscript.
	Fe^+2.345^	Like Fe+2.345, but with charge as superscript.
	Fe^2+^	Charge is rounded and superscripted with sign following the charge.
Charge	+2	Displays the charge (or formal oxidation number), as far as defined. Charge is rounded and signed even if positive.
	2	Charge is rounded and signed if negative.
	+2.345	Charge is signed even if positive but not rounded.
	2.345	Charge is signed if negative and not rounded.
(Individual text)		The label contains individual text which has to be entered or changed in the input field Individual text.


Bond Label Text

To define the text for a new bond label or to edit the contents of an existing bond label, use the controls in the Text group of the Add Bond Labels dialog box or the Edit Bond Labels dialog box, rsp. See the articles "Adding Labels" and "Changing Label Text, Style, or Size After Creation" how to add labels or how to edit existing labels, rsp.

The bond label can either have individual text or pre-defined text such as the bond length. Content determines the kind of information to be supplied, whereas Format decides how the information will be formatted. You may select from:

Content	Format	Description
Bond length	1.234	Formats the bond length in Angstroems without unit symbol.
	123.4	Formats the bond length in picometers without pm symbol.
	1.234 Å	Formats the bond length in Angstroems with unit symbol.
	123.4 pm	Formats the bond length in picometers with pm symbol.
	1.234(5)	Like 1.234 but with standard uncertainty, as far as defined.
	123.4(5)	Like 123.4 but with standard uncertainty, as far as defined.
	1.234(5) Å	Like 1.234 Å but with standard uncertainty, as far as defined.
	123.4(5) pm	Like 123.4 pm but with standard uncertainty, as far as defined.
Identifier	BOND #	The sequential number of the bond in the list of created bonds (beginning with #1).
(Individual)		The label contains individual text which has to be entered or changed in the input field Individual text.


Labels: Style, Size, and Position
Style, Size, and Position

To define the size, position, and style for a new atom or bond label or to edit the size, position, or style of an existing atom or bond label, use the controls in the Style group of the Add Atom/Bond Labels dialog box or the Edit Atom/Bond Labels dialog box, rsp. See the articles "Adding Labels" and "Changing Label Text, Style, or Size After Creation" how to add labels or how to edit existing labels, rsp.

Both size and position of an atom or bond label are defined in Angstroem units rather than in centimeters or millimeters, that means both position and size of the label depend on the current enlargement factor of the structure picture. If central projection is used, labels in the front may appear larger than those in the rear. If you rotate or shift a structure, the labels follow the movements of their associated atoms and bonds, rsp.

Defining the label's position

The position of an atom or bond label is defined as the vector between the reference point of the label and the center of the associated atom or the center of the associated bond, using the components x, y, and z in Angstroem units. x determines the horizontal, y the vertical distance. Positive values mean shift to the right and top rsp. The reference point of the label is defined by Alignment.

The third parameter, z, is used only for rendered structure pictures to define the 3D position of the text relative to the 3D coordinates of the corresponding atom or bond. Since rendered representation uses a Z buffer to calculate the overlap of objects, parts of a label may interpenetrate its associated atom or bond, if it is "too near". To avoid this, use a value of about 0.5 or higher to ensure drawing of the label in front of the atom or bond, rsp. Since x, y, and z refer to the view coordinate system, the label does not rotate with the atom or bond, when the structure is rotated.

The Alignment defines the reference point within the rectangle that surrounds the label text. The label may be aligned in different ways:

Centered	the horizontal and vertical center of the label
Right	the left edge and the vertical center (text appears right from the reference point)
Left	the right edge and the vertical center (text appears left from the reference point)
Parallel	the label text is rotated with the bond axis

Normally, labels do not rotate when the structure is being rotated. Especially for bond labels, you can assign an alignment that rotates bond labels automatically so that the text is parallel with the bond axis.

Defining the label size

Like the position, the size of the label text is defined in Angstroem units. The real size of the label (in centimeters) in the structure picture is calculate with the current enlargement factor. If central projection is used, labels in the front may appear larger than those in the rear. Changing the enlargement factor of the structure picture leads to a equivalent increase or decrease of the label size. Use the input field Text size to set the label text size.

Defining the label color

Use the color select box Color to select an existing color or define a new color for the label.

If you are adding new labels, you can constrain the label's color with the atom's or bond's main color, instead. For that, check the checkbox Use atom's main color. The main color is derived from the atom's or bond's design: The main color is the interior color of atoms and thick bonds. (For thin bonds, only one color is available.) If the atom or thick bond is hollow or has black or white as interior color, Diamond takes the edge color instead.

Defining font and other attributes

Push the Font button to open the MS Windows standard font dialog to define the font and attributes like bold and/or italics. If the text shall appear underlined, check the Underline checkbox. Use Strike out to strike out the text. If the checkbox Opaque is checked, the label text will be opaque, which means that the background of the label text will be filled with the current background color. Otherwise (default) it is transparent.

Defining a default style for labels

When you are editing an existing label, check the checkbox Use this design as default for new labels to make the current options (text, size, position, styles) the default settings for new labels. These default settings apply automatically, if you add labels with the quick method (compare "Adding Labels"). The checkbox is not available in the Add Atom/Bond Labels dialog.


Labels: Shifting Position With Mouse or Cursor
Shifting Position With Mouse or Cursor

You can shift the position of an atom label or bond label with the mouse. If you select multiple atom or bond labels, you can shift these labels simultaneously. Shifting the position means here changing the x and y coordinate of the label(s).

To shift a single label, move the mouse cursor into the rectangle that surrounds the label text, then press down the left mouse button and shift the label with left mouse button down to the desired position. When you have reached the desired position, release the left mouse button.

To shift multiple labels simultaneously, first select the labels, then move the mouse cursor into one the label markers, and continue like for a single label.


Changing Label Text, Size, or Style After Creation
Changing Label Text, Style, or Size After Creation

To edit the properties of one or more atom or bond labels, do the following:

If you want to edit one label, the easiest way is to double-click into the rectangle that surrounds the label text. Or click with the right mouse button into that rectangle, and then choose the Edit atom/bond label(s) command from the context menu, or choose the Atom labels or Bond labels command, rsp., from the Objects menu.

If you want to edit more than one label at a time, first select the labels, then either double-click into one of the markers or click with the right mouse button into one of the markers and choose the Edit atom/bond label(s) command from the context menu, or choose the Atom labels or Bond labels command, rsp., from the Objects menu.

All methods open the Edit Atom Labels dialog or Edit Bond Labels dialog, rsp.

If you edit one label only, change the settings you want to alter, and confirm with OK. If multiple labels have been defined, those settings keep blank that are not unique. If for example two labels have been selected with identical settings, but one label in red, the other in yellow, the color select box will be empty.

See the articles "Atom Label Text", "Bond Label Text", and "Style, Size, and Position" about label text, size, position, and style.


Removing Labels

To delete one or more atom or bond labels, select the labels, and then either press the Delete key, or click with the right mouse button into one of the markers, and choose the Destroy atom/bond label(s) command from the context menu.


Text: Overview

This chapter deals with the use of text in the structure picture and will tell you:

- what the text may contain and how to access bibliographic text,

- how to make use of text fields,

- how to define the size, position, and style of the text,

- how to shift the text with the mouse,

- how to change the contents, size, position, and style of an existing label text,

- how to delete text.


Adding Text

To enter a new text, push the [image] button in the Build toolbar, or use the "hotkey" Shift+Ctrl+T. All methods open the Add Text dialog. If you make use of the main menu, assure that no existing text has been selected, and choose the Text command from the Objects menu. (Otherwise the Edit Text dialog would be called.)

You can enter a new text in the Text combobox or access an existing text from the combobox list. Furthermore you can select from bibliographic data and insert the text directly or as text field. Read the articles "Contents of Text String" and "Using Text Fields" about the contents of a text string or the use of text fields.

Size, position and styles of the text can be defined in the Style group of the Add Text dialog.


Contents of Text String

A user-defined text can have any arbitrary contents, including special characters for text formatting (bold, super/subscript, etc.). You can access pre-defined text from bibliographic data either as copy or as text field.

To enter a new text or to edit an existing text, use the input field of the Text combobox in the Add/Edit Text dialog. You can access text strings that have previously been defined from the list of the combobox. (Diamond stores all texts that have been entered during a session.)

To copy a text from the bibliographic data of the current structure, push the Get button, which opens the Get Text dialog, where you select from several bibliographic data, such as title, structural formula, authors' names, etc. as well as from generated data, such as formula sum, Pearson code, etc. The selected text can either be inserted into the Text combobox of the Add/Edit Text dialog directly as copy, or as text field. A text field has the advantage that the text is automatically updated if the corresponding bibliographic data has changed.

You will get more information about the data you can select from and the syntax of text fields from the article "Using Text Fields".


Using Text Fields

A text field has the form "{FIELD=<FIELDNAME>}", e.g. "{FIELD=FORMULA_SUM}" for the formula sum. The following field names are available:

<FIELDNAME>	Description
TITLE	the title of the publication or of the compound,
AUTHORS	the name(s) of the author(s),
NAME_COMMON	the common (usual, trivial) name of the compound,
NAME_SYSTEMATIC	the systematic (IUPAC) name of the compound,
NAME_MINERAL	the mineral name of the compound,
NAME_STRUCTURETYPE	the name of the structure type,
FORMULA_SUM	the formula sum, which has been generated from the atomic parameter list,
FORMULA_STRUCTURAL	the structural formula, which is defined as bibliographic data,
FORMULA_ANALYTICAL	the analytical formula, which is defined as bibliographic data,
FORMULA_TYPE	the formula type, which has been generated from the atomic parameter list,
PEARSONCODE	the Pearson symbol, which has been generated from the atomic parameter list and the current space group,
WYCKOFFSEQUENCE	the Wyckoff sequence, which has been generated from the atomic parameter list.

Text fields have the advantage that they will be updated automatically when the structural data have been changed, whereas invidual text is not updated.

Individual text and text fields may be mixed together, e.g. "Formula: {FIELD=FORMULA_STRUCTURAL}"


Text: Style, Size, and Position
Style, Size, and Position

The position of a text refers to the center of the structure window (or structure picture rsp.). That means text does not move if the structure is shifted or rotated. Both position and size use centimeters dimension. Thus the size of the text does not vary with the enlargement factor.

Text position

You define the horizontal (left input field of Position...) and vertical (right input field) distance of the reference point of the text string from the center of the picture (or from the center of the structure window, rsp.), in centimeters. Positive values mean shift to the right and top rsp. The reference point of the text string is the left edge of the first character and the baseline of the text.

Text size

Define the text size in centimeters in the input field Text size. The size is the height of a character cell of the text in centimeters. This is the vertical distance between bottom and top line of the font.

Text color

Select the color for the text from the color select box.

Text font and other attributes

Use the Font button to calls the MS Windows standard font dialog to define the font and attributes like bold and/or italics. If the Underline checkbox is checked, the label text will be underlined. If the Strike out checkbox is checked, the label text will be struck out.


Text: Shifting Position With Mouse or Cursor
Shifting Position With Mouse or Cursor

You can shift the position of a text with the mouse. If you select multiple texts, you can shift these texts simultaneously. Shifting the position means here changing the horizontal and vertical position of the text(s) relative to the center of the structure window or picture.

To shift a single text, move the mouse cursor into the rectangle that surrounds the text, then press down the left mouse button and shift the text with left mouse button down to the desired position. When you have reached the desired position, release the left mouse button.

To shift multiple texts simultaneously, first select the texts, then move the mouse cursor into one the text markers, and continue like for a single text.

You can create a copy of an existing text at the target position, that means you copy a text instead of moving it. For that, hold down the Ctrl key when you press down the left mouse button and continue like for a single text.


Changing Text, Style, or Size After Creation

To edit the properties of one or more existing texts, do the following:

If you want to edit one text, the easiest way is to double-click into the rectangle that surrounds the text. Or click with the right mouse button into that rectangle, and then choose the Edit text(s) command from the context menu, or choose the Text command from the Objects menu.

If you want to edit more than one text at a time, first select the texts, then either double-click into one of the markers or click with the right mouse button into one of the markers and choose the Edit text(s) command from the context menu, or choose the Text command from the Objects menu.

All methods open the Edit Text dialog.

If you edit one text only, change the settings you want to alter, and confirm with OK. If multiple texts have been defined, those settings keep blank that are not unique. If for example two texts have been selected with identical settings, but at different positions, the input fields for the position will be empty.

See the articles "Contents of Text String", "Using Text Fields", and "Style, Size, and Position" about contents, size, position, and style of a text.


Removing Text

To delete one or more texts, select the texts, and then either press the Delete key, or click with the right mouse button into one of the markers, and choose the Destroy text(s) command from the context menu.


Legend of Atom Types: Overview

A legend listing all atom types of the current structure can be displayed at an arbitrary position of the structure picture.

"Settings" describes how to switch on or off the display of the legend, to define the position, size and other settings.

The article "Relative vs. Absolute Positioning" compares between the two kinds of positioning the legend.


Legend of Atom Types: Settings

You define all settings for the legend of atom types in the Legend dialog. To open this dialog, choose the Legend command from the Objects menu. If the legend is still displayed, you can also open the dialog with a double-click into the legend.

Switching the legend on or off

The main switch in the Legend dialog is the checkbox Display legend. This determines if the legend is displayed or not. If not, all other controls in the dialog box are unavailable.

Position of the legend

The position of the legend refers either to the center of the structure picture of to one of the four corners. This is defined by the setting in the combo box Relative to:

center of picture	the values in X and Y define the horizontal and vertical distance of the centerpoint of the legend from the center of the structure picture or the center of the structure window, rsp., in centimeters.
top left	the values in X and Y define the horizontal and vertical distance of the upper left corner of the legend from the upper left corner of the structure picture or the structure window, in centimeters. This means, the position of the legend depends on the size of the structure window (or of the page, if page view mode is used or when printed).
top right	the values in X and Y define the horizontal and vertical distance of the upper right corner of the legend from the upper right corner of the structure picture or the structure window, in centimeters.
bottom left	the values in X and Y define the horizontal and vertical distance of the lower left corner of the legend from the lower left corner of the structure picture or the structure window, in centimeters.
bottom right	the values in X and Y define the horizontal and vertical distance of the lower right corner of the legend from the lower right corner of the structure picture or the structure window, in centimeters.

The position of the legend relative to the center or a corner of the structure window or picture is defined in the two input fields Position X and Y, rsp. These values are given in centimeters. Positive values grow to the right and top rsp., negative values to the left and bottom rsp.

Size of the legend

The size of the legend is indirectly determined by the sum of the radii for the atoms to be displayed in the legend. From the combo box Atomic radii, you can choose between two kind of radii:

fixed	All atoms in the legend have the same size (the radius is given in Radius in centimeters).
atom-type-specific	The radii are used which have actually been used for drawing, that means the legend's size depends on the current enlargement factor.

If you are using a "fixed" radius, every atom that is displayed in the legend, will use the radius given in the input field Radius in centimeters. Otherwise the radius depends on the real atom type and increases or decreases when the enlargement factor is changing.

The same legend of atom types: The upper one using fixed radii (0.25 cm, font: 0.5 cm), the lower one with "atom-type-specific" radii and an enlargement factor of about 0.85 cm/Å.

Settings for the atom type label text

To change the font used for the atom type label text, push the Font button. The size of the text is determined by the value in the input field Font size in centimeters. Please note that the point size field of the font in the MS Windows standard font dialog will be ignored. The attributes bold and italics will be ignored, too. The color of the text is defined by the color select box Color.

Color and thickness of legend's border

The color of the legend's border is determined by the color select box Color, that means the font uses the same color as the border. The thickness in millimeters is given in the input field Border width. Use a value of zero, if you want no border to be drawn.

Formatting the atom type symbols

Diamond accesses the symbols that have been defined with the atom types. (Usually these are default symbols made up from element symbol plus charge as far as defined. To change an atom type symbol, see "Atom Types".) If the atom type symbol begins with an element symbol, the rest of the symbol can be superscripted or subscripted, according to the setting in the combo box Symbols:

(no re-formatting)	The atom type symbol is not re-formatted.
superscript extension	If the atom type symbol consists of an element symbol and an attached extension (e.g. the oxidation number), the extension will be superscripted.
subscript extension	dito, but subscripted.

With the Select button, you can open the Select Atom Types for Legend dialog and choose, which atom types may appear in the legend or if only those atom types with at least one corresponding created atom in the structure picture will be listed (checkbox Hide atom types not used in structure picture). Otherwise, all atom types of the atom type list will be listed.


Legend: Relative vs. Absoulte Positioning
Legend: Relative vs. Absolute Positioning

The position of the legend of atom types refers to either the center of the structure picture (or the structure window, rsp.) or to one of its four corners. If you want to align the legend to special objects of the structure picture, you should set the combo box Relative to to "center of picture". In this case the position remains even if you change the window's size or if you print the structure picture. When using relative positioning, the legend's position adjusts automatically to its window's size. That leads to different absolute positions of the legend on screen and printout rsp.

The following screenshots compare the different results of relative positioning for the structure window (upper part) and for the printout (lower part; the printout is simulated by the page view mode). In both case the lower right corner of the legend is fixed with the lower right corner of the structure window and printout, rsp.


Coordinate System: Overview

A coordinate system displaying the current orientation of the current structure can be displayed at an arbitrary position of the structure picture.

"Settings" describes how to switch on or off the display of the coordinate system, to define the position, size and other settings.

The article "Relative vs. Absolute Positioning" compares between the two kinds of positioning the coordinate system.


Coordinate System: Settings

You define all settings for the coordinate system representing the current orientation of the current structure in the Coordinate System dialog. To open this dialog, choose the Coordinate system command from the Objects menu. If the coordinate system is still displayed, you can also open the dialog with a double-click into the rectangle that surrounds the coordinate system.

Switching the coordinate system on or off

The main switch in the Coordinate System dialog is the checkbox Display coordinate system. This determines if the legend is displayed or not. If not, all other controls in the dialog box are unavailable.

Position of the coordinate system

The position of the legend refers either to the center of the structure picture or to one of the four corners. This is defined by the setting in the combo box Relative to:

center of picture	the values in X and Y define the horizontal and vertical distance of the origin of the displayed coordinate system from the center of the structure picture or the center of the structure window, rsp., in centimeters.
top left	the values in X and Y define the horizontal and vertical distance of the origin of the displayed coordinate system from the upper left corner of the structure picture or the structure window, in centimeters. This means, the position of the coordinate system depends on the size of the structure window (or of the page, if page view mode is used or when printed).
top right	dito, but referring to the upper right corner instead.
bottom left	dito, but referring to the lower left corner instead.
bottom right	dito, but referring to the lower right corner instead.

The position of the coordinate system relative to the center or a corner of the structure window or picture is defined in the two input fields Position X and Y, rsp. These values are given in centimeters. Positive values grow to the right and top rsp., negative values to the left and bottom rsp.

Style of the coordinate system

The coordinate system either represents the axes of the reference coordinate system or of the crystal coordinate system. Select the system from the Labels combo box:

a, b, c	The axes represent the axes of the crystal coordinate system, i.e. the cell vectors a, b and c.
x, y, z	The axes represent the axes of the reference coordinate system.

If the checkbox Arrowheads is checked, arrowheads are assigned to the tops of the axes of the coordinate system.

Size of the coordinate system

The input field Axes' lengths defines the maximum length of an axis of the coordinate system given in centimeters, that means the size of the coordinate system. An axis has maximum length if it is arranged parallel to the drawing area, else it is shorter corresponding to its projection.

The input field Axes' thickness defines the thickness of the lines which represent the axes, in millimeters.

Font and color

To change the font used to label the axes with 'a', 'b', and 'c' or 'x', 'y', and 'z', rsp., push the Font button, which opens the MS Windows standard font dialog. The size of the text is determined by the value in the input field Font size in centimeters. Please note that the point size field of the font in the MS Windows standard font dialog will be ignored. The attributes bold and italics will be ignored, too. The color for both text and axes is defined by the color select box Color.


Coordinate System: Relative vs. Absolute Positioning

Like for the legend of atom types, the position of the coordinate system that represents the current orientation of the current structure either refers to the center of the structure picture (or the structure window, rsp.) or to one of its four corners. If you want to align the coordinate system to special objects of the structure picture, you should set the combo box Relative to to "center of picture". In this case the position remains even if you change the window's size or if you print the structure picture. When using relative positioning, the position of the coordinate system adjusts automatically to its window's size. That leads to different absolute positions of the coordinate system on screen and printout rsp.

The effect is in principle the same as for the legend of atom types. For that compare the two screenshots in the article "Relative vs. Absolute Positioning".


Optimizing the Representation of the Structure Picture: Overview

The expression of a structure picture appears quite different dependent on the output device. A rendered picture on the screen (with dark background) may give quite impressive results, whereas the printout of this picture on a black-and-white printer (with white background) will look rather modest.

For different output devices, Diamond offers several functions to optimize the structure picture.

The optimization can be done with the Auto Format Function.


Different Targets to Optimize for

The expression of a structure picture appears quite different dependent on the output device. A rendered picture on the screen (with dark background) may give quite impressive results, whereas the printout of this picture on a black-and-white printer (with white background) will look rather modest.

For different output devices, Diamond offers several functions to optimize the structure picture:

Rendered representation

In most cases, rendered representation yields the best result for a structure picture, especially when dark background is used. If you print such a picture on a normal black-and-white printer and use the default setting (which does not cover the background of the printout with the original dark background color of the screen), the result may be disappointing. The main reason is that rendered representation uses no edges, and that will lead to low contrast between the white background and the grey-rasterized objects.

You will get better results on a color printer - even on white background -, but the best results on a high-end color printer, such as a thermo-sublimation printer, when you use the original background color. For that, you must switch out the default setting "Print black-on-white", which uses black-on-white mode by default for printing.

Colored flat representation

If you use flat representation, you may need auxiliary effects to enhance the 3D impression of the results on screen or printout. If you make use of objects filled with colors, especially atoms and thick bonds, you need to define a (dark) edge for a better contrast between white background and the interior colors of the objects, especially if you convert this graphics to black-on-white later.

Diamond offers several options to represent a flat colored picture:

- with light bulbs for a lighting impression on atom spheres.

- dito, but without light bulbs.

- dito, without light bulbs, and with black edges.

The third of these options (introducing black edges to the objects) is quite good for gray-scaled printouts on a black-and-white printer of color printouts on a color printer.

Gray-scaled output

Diamond can convert the colors used to fill atoms, thick bonds, and polyhedron faces to gray tones with the corresponding brightness. All lines will become black. If objects have no edges already, they will get black edges.

Pure black-and-white representation

This kind of representation uses only black lines to draw the structure picture. Colored interior (atoms, thick bonds, polyhedron faces) become white. This kind of representation does not convert colors to gray tones. This is the best method to avoid loss of quality when black-and-white printouts are reproduced on a copier with rather low quality.


Auto Format Function

To make use of Diamond's Auto Format function, choose the Auto format command from the Tools menu, which opens the Auto Format dialog.

Define what the structure picture is to be optimized for in the Destination group:

Rendered representation (highest quality)	Switches to rendered representation, activates lighting and depth cueing. Switches black-on-white mode off.
Light bulb representation on dark background	Uses flat representation, activates lighting (for the light bulbs) and depth cueing. Switches black-and-white mode off.
Flat colored objects on dark background	Uses flat representation. Switches lighting, depth cueing, and black-and-white mode off.
Flat colored objects with black edges on white background	Uses flat representation. Switches lighting and depth cueing off. Switches to black-and-white mode. The designs of atoms, thick bonds, and polyhedron faces are adjusted to have black edges for a better contrast on white background.
Gray-scaled objects on white background	Works like the previous option, but all lines will become black, and all filling colors converted to gray-scales.
Pure black-and-white representation on white background	Works like the previous option, but all atoms, thick bonds, and polyhedron faces will not be filled (that means they have white interior).

Normally, the changes apply only to the created atoms, bonds, and coordination polyhedra. If you want to update the atom type designs, bond type designs as well as the default design for new polyhedra, check the corresponding checkboxes:

- Update atom type designs

- Update bond type designs

- Update standard polyhedron design


Coordination Polyhedra: Overview

Coordination polyhedra serve for the characterization of an atom’s neighbourhood. They are built by connecting the centers of coordinated atoms by lines. More complex structure units can be described by a framework of connected polyhedra. Two polyhedra can be connected by a common corner, a common edge or a common plane.

Diamond supports the creation and display of convex coordination polyhedra and treats them as individual objects within the ball-and-stick model rather than as an independent model.

In this chapter, you will find articles

- about features and limitations,

- how to create coordination polyhedra,

- how to select the atom types for central and ligand atoms,

- about the difference between generic and fixed spheres,

- how to define polyhedra with polygons that are not triangular,

- how to define a polyhedron without central atom,

- about designs for coordination polyhedra,

- how to use hatching on the polyhedron faces,

- how to display polyhedra with front faces open,

- about global settings for all polyhedra,

- how to select existing polyhedra,

- how to change the designs of existing polyhedra,

- how to delete polyhedra.


Coordination Polyhedra: Features and Limitations

Diamond can construct polyhedra with up to 128 ligand atoms. Each polygon (polyhedron face) can have up to eight corners (and must have at least three corners, of course), but it must be convex. There is in principle no limit for the maximum distance between central point and ligand atom.

Polyhedron faces can be partially opened as well as being transparent, with or without edges and with or without hatching.

Example: Polyhedron framework of Sodalite with rectangular and hexagonal polygons and with partially open faces. The Diamond Tutorial will show you how to build up such a framework.

Reference:

Name

Sodium tecto-alumoberyllotetrasilicate chloride (8/2/2)

Formula

Na8 (Al Be Si4 O12)2 Cl2

Author(s)

Hassan I, Grundy H D

Title

The crystal structure and thermal expansion of tugtupite, Na8(Al2Be2Si8O24)Cl2

Journal

CAMIA 29 (1991), pp. 385 - 390

Mineral name

Tugtupite - from Ilimaussaq, South Greenland

Comment

TEM 1178

Example 2: Two representations of a fullerene molecule (C60) as polyhedron with no central atom and hexagonal and pentagonal faces. The left version in flat representation with some faces open and the other hatched, the right version using transparent faces (transparency factor: 0.5).


Creating Coordination Polyhedra

In Diamond, every coordination polyhedron is addressed by its central atom. If there is no atom in the parameter list that can serve as central atom, you may define a dummy atom as central atom. One atom can only be center of one polyhedron; it cannot be center of multiple polyhedra.

There are in principle two different modes to create polyhedra:

a) The semi-automatic creation, where Diamond searches for the coordinating atoms within a given enclosure sphere and creates these atoms, if necessary.

b) The manual creation, where you select the atoms that will become corners of the polyhedron. In that case, Diamond searches for a suitable central atom or creates a dummy atom, when there is no suitable atom in the parameter list.

Manual creation is only possible if at least three atoms have been selected. With three or more selected atoms, you will be prompted for the polyhedron building mode, where you have the choice to create N polyhedra with the N selected atoms as centers or to create one single polyhedron with the N selected atoms as corners.

Semi-automatic creation

There are several ways to create coordination polyhedra using the semi-automatic method:

1. The easiest way is to construct polyhedra around selected (central) atoms, using default settings. For that, select one or more atoms, and then either push the [image] button in the Build toolbar or use the "hotkey" Shift+Ctrl+H. If three or more atoms are selected, you will be prompted for the polyhedron building mode, where you must choose the option Use selected atoms as central atoms and confirm with OK.

2. If you must change the default settings, especially the size of the polyhedron sphere, you select one or more (central) atoms, then click with the right mouse button into one of the selected atoms, and choose the Add polyhedra command from the context menu, or choose the Polyhedra command from the Objects menu.

3. The third way works without selected central atoms. (No atom must be selected in this case!) You select the central atoms indirectly from an atom type list. (If you add polyhedra to selected atoms, this list is not available.)

All three ways open the Add Polyhedra dialog unless you have used the button in the Build toolbar mentioned above. For informations about the selection of atom types, the sphere type and size, etc. read the following articles "Selecting Atom Types" and "Using Fixed or Generic Spheres".

Manual creation

This polyhedron building mode is only available if at least three atoms have been selected. If you start the polyhedron creation with one of the options mentioned under "Semi-automatic creation", you will be prompted for that polyhedron building mode. Choose the option Construct one single polyhedron from selected atoms and confirm with OK, which will open the Build Polyhedron dialog, where you can select an atom from the parameter list or a new dummy atom to become the central atom of the polyhedron, the epsilon value as well as the design for the new polyhedron. The polyhedron will be built after you confirm the dialog with OK.


Coordination Polyhedra: Selecting Atom Types

If no atom has been selected and you have chosen the Polyhedra command from the Objects menu, you will get the Add Polyhedra dialog.

This dialog will offer two lists, both containing all atom types of the current structure. All created atoms that belong to one of the atom types in the list Central atoms will be taken as central atoms of coordination polyhedra. The second list, Ligand atoms, is used to select those atom types that will become ligand atoms of the polyhedron spheres.

Add Polyhedra dialog for a structure with atom types Fe+3, Mn+2, P+5, and O-2. The atom types Mn+2 and P+5 have been selected as central atoms, the coordination polyhedra shall be made up of oxygen atoms.

If you want to build polyhedra with central atoms that have been selected from the parameter list rather than the atom type list, or use only selected atoms from the parameter list as ligand atoms, you can derive a new atom type from one of the existing atom types. See the article "Assigning a New Atom Type at Runtime" how to define a new atom type.


Coordination Polyhedra: Using Fixed or Generic Spheres

The sphere of the coordination polyhedra can either have fixed dimensions, given by a minimum and maximum distance value, or can be variable ("generic"). This kind of distinguishing can be compared with that for fixed spheres and coordination spheres.

You can choose between fixed and generic sphere in the Add Polyhedra dialog in the Type of sphere group:

Generic	The size of the sphere (inner and outer bound) depends on the types of central and ligand atom and is defined in the connectivity.
Fixed	Inner and outer bound of the sphere are defined by RMin and RMax in Angstroems.

The generation of coordination polyhedra works with completed as well as incomplete coordination spheres. That means missing ligand atoms will be supplemented if necessary. Generic spheres are used to create ligand atoms which are bonded to the central atom. The dimensions of these spheres are defined in the connectivity list and vary thus from atom type pair to atom type pair. The polyhedra procedure does not generate ligand atoms that are selected in the list Ligand atoms but are not selected as bonded in the connectivity list. If fixed spheres are used, even such ligand atoms will be created that are not defined as bonded in the connectivity list.


Coordination Polyhedra: Getting Polygons Greater Than Triangles

When Diamond builds a polyhedron, it collects all ligand atoms within the defined fixed or generic sphere, and constructs triangular polygons.

As far as these triangles build obtuse angles of intersection, they are united to polygons by removing the common intersection lines. Diamond uses an epsilon value for this angle to decide if four or more points define a larger polygon or if two or more triangles must not be united. The angle can be edited in the input field Angle epsilon in the Add Polyhedra dialog or in the Build Polyhedron dialog. The default value is one (degrees). You may enlarge it if the coordination differs significantly from ideal relations.


Polyhedra With No Central Atom

In Diamond, you can define no coordination polyhedron without a central atom. If there is no atom in the structural parameters that can be used as central atom, you can define a dummy atom for the center. The dummy atom will be added to the atoms in the parameter list but has no chemical meaning. The dummy atom will also be added to the list of atom types, and thus also to the list of bond types, where you can change the basic behaviour for all atoms derived from that dummy atom (atoms' style, bonding sphere, etc.)

The easiest way to create a dummy atom is to select all atoms that will build the polyhedron, that means the atoms in the coordination sphere, and then create an atom in the center of those selected atoms. The article "How to Insert an Atom" describes in principal how to create a dummy atom in the center of selected atoms. Since the dummy atom is automatically created at the new position and is appended to the list of atom types, you can create a polyhedron using one of the methods described in "Creating Coordination Polyhedra" and "Selecting Atom Types".

The picture shows a fulleren molecule (C60) as polyhedron with a dummy atom in its center:


Coordination Polyhedra: Designs

The design of a polyhedron face is made up of the following settings:

Style	Defines if the faces are open, partially open or closed.
Interior color	Defines the color that is used to fill the interior of the polyhedron faces.
Interior brush	Offers several options for the interior, like hatching, transparency, etc.
Edge color	Defines the color that is used to draw the edge of the polyhedron face.
Edge pen	Offers several options for the edge, like a dotted edge or no edge.
Edge thickness	Defines the line thickness for the edge or zero if no edge shall be drawn.
Specular and emissive reflectivity, shininess	Defines the behaviour of the polyhedron faces in rendered representation.
Transparency	Offers transparent faces in rendered representation.
Hatching	Offers real 3D hatching. For details, see "Hatching".

Since rendered representation uses neither edges nor patterns or hatching, some of the above settings will be used only in flat representation.

To define the design for new polyhedra, push the Design button in the Add Polyhedra dialog. Furthermore you can change the designs of existing polyhedra.

The Design page of the Design for new polyhedra dialog

The design of a polyhedron is described in the following:

Style

The polyhedron style determines if the polyhedron faces are all closed, all open or partially open. The style is defined in the Style combobox.

Open faces	All faces will be displayed open.
Front open	Back faces will be drawn closed, front faces open or closed. A face will be drawn transparent (open), if its normal vector encloses an angle less than the angle defined in Opening angle with the z-axis of the view coordinate system.
Closed faces	All faces will be displayed closed.

Interior of the polyhedron faces

Like for atoms or thick bonds, you can define a color and a brush for the interior of the polyhedron faces. Furthermore you can assign the central atom's main color, if you check the Use central atom's main color as interior color checkbox (which makes the individual color not unavailable). The main color is derived from the central atom's design: The main color is the interior color of an atom If the atom is hollow or has black or white as interior color, Diamond takes the edge color instead. If you do not use the central atom's main color, you can select a color from the color select box Color. The brush can be selected from the Brush combo box:

Solid	The default setting. The interior is filled opaque with the interior color.
Transparent	The interior of the polyhedron face is not filled.
Background	The interior color is ignored, and the background color is used instead.
Hatching 1, 2,...	The interior is filled opaque with the interior color, and a hatching is used with the pattern color. Please note that standard MS Windows hatching brushes are used for this option, which depends on the resolution of the output device. That means the density of lines is much more higher on a 600 dpi printer than on the screen (about 100 dpi). It is not recommended to use this kind of hatching; you should make use of the 3D vector hatching instead.

Edge of the polyhedron faces

You may define an edge for the polyhedron faces or not. The thickness of the edge is defined in millimeters in the Thickness input field. The color is selected from the Color select box in the Edge group. The pen can be selected from the combo box Pen:

Solid	The default setting. The edge is drawn as solid line with the edge color and the given thickness in millimeters.
Dash	The edge is drawn as dashed line with the edge color, whereas the thickness is ignored.
Dot	The edge is drawn as dotted line with the edge color, whereas the thickness is ignored.
No edge	Draws no edge.
Background	Draws the edge solid, but ignores the edge color and uses the background color instead.

Material properties

The Material page of the Design For New Polyhedra dialog offers you several material properties for the rendered representation of polyhedron faces. In principle these settings behave like for atoms and thick bonds; compare the article "Material Properties". Material properties take no effect for flat representation.


Coordination Polyhedra: Hatching

In flat representation mode, you can use real 3D hatching for the polyhedron faces. Unlike the pre-defined MS Windows hatched brushes, this kind of hatching is done by drawing 3D lines across the polyhedron faces. These hatching lines are oriented against a hatching vector to define the preferred orientation of the hatching lines to be parallel with the polygon edges.

Hatching is not used in rendered representation mode.

Hatching is defined on the Hatching page of the Design For New Polyhedra dialog and the Edit Polyhedra dialog, rsp.

Selecting hatching

The combo box Style defines if and what faces are to be hatched. You may choose one of the following settings:

No hatching	None of the faces will be hatched.
Front faces only	Front faces will be hatched but not back faces. This option is useful for either closed or front open polyhedra.
Back faces only	Back faces will be hatched but not front faces. This option is useful only for front open polyhedra, since only these enable a view to the back faces.
All faces	All faces will be hatched.

Orientation of hatching

For each polyhedron face (polygon), the hatching lines are parallel to one of the polygon's edges. When Diamond selects this edge, it uses that edge that is at most vertical with the "hatching vector". The three components of the hatching vector are defined in the input fields Vector, X... The three components of the vector refer to the reference coordinate system. The distance between the (parallel) hatching lines is given in Angstroems in the input field Distance. When you change the enlargement factor the distance increases and decreases with the corresponding amount.

Relative length for each hatching line

If this value in the input field Relative length... is 1 (default value), the hatching lines touch the polyhedron edges. With a value between 1 and 0 these lines will be drawn shorter. E.g. with a value of 0.8, 10 percent at each end of the line will be omitted. This option may be used to contrast with the polyhedron edges.

Style, color, and thickness of the hatching lines

The color of the hatching lines is defined by the color select box Color, whereas the combo box Pen defines, if and how lines will be drawn. The input field Thickness defines the thickness of solid hatching lines in millimeters. Please note that "dashed" and "dotted" lines will use only one pixel of thickness, regardless what is defined in Thickness.

Two illustrations of a Si-O tetrahedron in alpha-quartz. Both with a hatching distance of 0.3 Angstroems. The left picture uses the default value for the "Relative length of each hatching line" of 1.0, the right one a value of 0.95, so that the hatching lines do not touch the polygon edges.


Displaying Polyhedra With Front Faces Open

Since you must select polyhedra via the associated central atom, you may get problems when you use of polyhedra with closed faces (the regular case). It may be difficult and tedious to match the invisible central atom for selecting.

To avoid this, Diamond offers a function that hides temporarily all front faces of all polyhedra. Please note that this does not change the polyhedron style from close faces to front faces open, and this property will not be saved with the Diamond Structure Document. When all front faces have been opened, you can easily access the polyhedra's central atoms.

To open polyhedron faces temporarily, push the [image] button in the Display toolbar, or choose the Hide command from the Display menu, and check the Hide front faces of all polyhedra checkbox in the Hide dialog.

The Sodalite example with temporarily open polyhedron faces.


Global Settings For All Polyhedra

While most of the settings can be defined individually for each coordination polyhedron, some settings apply globally to all polyhedra. To change these settings, push the Options button in the Design For New Polyhedra dialog or Edit Polyhedra dialog, rsp., which opens the Global Settings For Polyhedra dialog. These settings are:

Darken back faces	If this checkbox is checked, the back faces are drawn darker than front faces. This makes it easier to distinguish between front and back faces if polyhedra are particularly open.
Show internal bonds	If this checkbox is checked, bonds (as far as defined) between central atom and ligand atoms will be drawn. This setting is not useful for closed polyhedra.
Ligand atoms reducing factor	Defines a factor between 0.0 and 1.0 that reduces the radii of all atoms which are ligand atoms of any polyhedra. That means a value of 1 does not have any influence to the atoms' original sizes, whereas a value of 0 suppresses these atoms completely.

The structure of alpha-quartz, both using Si-O tetrahedra. The left picture uses a ligand atoms reducing factor of 0.3, the right one a factor of zero, which means that no ligand atoms are drawn.


Selecting Polyhedra

If you select coordination polyhedra, you must select the associated central atom. Then choose the appropriate command from the context menu, for example "Edit polyhedra" or "Destroy polyhedra". With the help of the data pane, you can select coordination polyhedra from a list.

To open the list of polyhedra, choose the Polyhedra command from the List submenu of the Display menu. The list of polyhedra may contain informations about:

- the sequential number of the polyhedron (beginning with 0),

- the sequential number of the central atom in the list of created atoms (beginning with 0),

- the symbol of the central atom, as defined in the parameter list,

- the number of ligand atoms,

- the number of polyhedron faces (polygons),

- the distance (in Angstroems) between central and the closest ligand atom,

- the distance (in Angstroems) between central and the ligand atom which has the largest distance.

Example: Unit cell of Laueite (from Inorganic Crystal Structure Database; Collection Code: 23819) with purple tetrahedra around P and grey and brown octahedra around Mn and Fe in the structure picture and the list of all polyhedra in the data pane, sorted for atom symbols.

Reference:

Name

Diiron(III) manganese bis(phosphate) dihydroxide octahydrate

Formula

Fe2 Mn (P O4)2 (O H)2 (H2 O)8

Author(s)

Zur Kristallstruktur des Laueits, Fe2 Mn (P O4)2 (O H)2 (H2 O)8

Title

Zur Kristallstruktur des Laueits, Fe2 Mn (P O4)2 (O H)2 (H2 O)8

Journal

NATWA 11 (1954), pp. 256 - 256

Mineral name

Laueite


Coordination Polyhedra: Changing Designs After Creation

You can change the design of existing polyhedra. That means you may alter colors, edge, hatching, material properties and the style (which faces to open). But you cannot change the coordination sphere of a polyhedron, that means you cannot change the composition of the polyhedron (ligand atoms, geometry, etc.). If you want to change the composition, you must first destroy the polyhedron, and then create a new one with new settings concerning sphere size or what so ever.

Select the polyhedron (or multiple polyhedra at one time), and then choose the Edit polyhedra command from the context menu or choose the Polyhedra command from the Objects menu. Both ways open the Edit Polyhedra dialog, which works in principal like the Design For New Polyhedra dialog. For that refer to the articles "Designs" and "Hatching".


Destroying Polyhedra

Since you must select a polyhedron indirectly via its associated central atom, first select the central atom(s) of the polyhedra to be deleted, and then choose the Destroy polyhedra command from the context menu, or push the [image] button from the Build toolbar. You can easily select polyhedra from the polyhedron list in the data pane. Please refer to the article "Selecting Polyhedra" how to select polyhedra.


About control characters in text strings

The character strings you use for user-defined text in the structure picture may contain several control characters for formatting. DIAMOND works with control characters using CIF as well as ICSD nomenclature.

1. Superscript and subscript

The "^" character switches the superscription on or off rsp. There may be multiple characters between the "^" characters, e.g. "Na^+^" or "Fe^2+^". In ICSD format the character combination "$%" leads to the superscription of the one following character. For each superscripted character the character combination "$%" must be repeated.

The corresponding characters for subscription are "~" and "$/" rsp.

2. Greek letters

Letters of the greek alphabet are introduced by a back slash, followed by an uppercase or lowercase letter, e.g. "\g" for a lowercase "gamma", "\G" for an uppercase "Gamma". This table (from: Acta Cryst. (1991), A47, 655-685) gives you a survey:

\a	\A	alpha

\b	\B	beta

\c	\C	chi

\d	\D	delta

\e	\E	epsilon

\f	\F	phi

\g	\G	gamma

\h	\H	eta

\i	\I	iota

\k	\K	kappa

\l	\L	lambda

\m	\M	my

\n	\N	ny

\o	\O	omikron

\p	\P	pi

\q	\Q	theta

\r	\R	rho

\s	\S	sigma

\t	\T	tau

\u	\U	ypsilon

\w	\W	omega

\x	\X	xi

\y	\Y	psi

\z	\Z	zeta

In ICSD format the sequence "$+" introduces an uppercase, but "$-" a lowercase greek letter. The greek letter itself is written out, e.g. "$-gamma".

3. Special characters

You may use special characters, i.e. characters not belonging to the ASCII code set, without circumscribing, e.g. "ê", "Ç", "Å" etc. These special characters will be stored in the Diamond structure file (DSF) in ANSI format, but converted for CIF and vice versa, e.g. the Angstroem symbol is writte as "\%A" in CIF format.


Info Mode: Overview

Diamond offers a special mode where you can get informations about a selected object. To enter this info mode, push the [image] button in the Standard toolbar. The mouse pointer will then change to an arrow with the letter 'i'. Now you can click with the left mouse button on single objects. (Multiple or extended selection is not possible in this mode.) The informations depend on the clicked object.

Example: Screenshot of info mode with informations for a selected atom.

To end the info mode, either push the info mode button in the toolbar again, or simply press the Escape key, instead. The mouse cursor will return to its standard arrow symbol.

You can copy the information to the clipboard, if you select the lines you want to copy and then push the Copy button in the Object Info dialog.

Informations about a selected atom

Atom no.	Defines the index of the created atom in the list of created atoms. The first index is zero.
Symbol	Symbol of the atom of the parameter list, where the created atom has been derived from.
Chemical composition	Element symbol (plus attached hydrogen atoms as far as defined), followed by the oxidation number in parentheses (as far as defined). If the site occupation factor is defined but not 1, this factor follows the symbol. If the created atom is on a mixed site, element symbols, oxidation numbers and site occupation factors of all atoms on the mixed site will be enumerated.
Atom type	The symbol of the associated atom type.
Original coordinates	The fractional coordinatesref_coord of the atom in the parameter list, which the created atom has been derived from.
Atom code (no., symmetry)	The atom code of the created atom and (in parentheses) zero-based index of the atom from the parameter list as well as the symmetry operation that generated the atom.
Crystal coordinates	The crystal coordinates of the created atom.
Reference coordinates	The reference coordinates of the created atom.
View coordinates	The view coordinates of the created atom.

Informations about a selected bond

Bond no.	Defines the zero-based index of the bond in the list of created bonds.
Atom symbols	Symbols of the atoms of the parameter list, where the created atoms which are connected with this bond, have been derived from.
Atom code 1 (no., symmetry)	The atom code of the first created atom which is connected with the second atom, and (in parentheses) zero-based index of the atom from the parameter list as well as the symmetry operation that generated the atom.
Atom code 2 (no., symmetry)	dito for the second atom.
Bond length	The bond length, given in Angstroems.

Informations about a selected atom label

Atom label no.	Defines the zero-based index of the atom label in the atom label list.
Label text	The contents of the atom label.
Label size	The size in Angstroems of the label.
Label position (x, y, z)	The 3D position of the label relative to the center of the associated atom.
Atom no.	The zero-based index of the associated atom in the list of created atoms.
Symbol	The symbol of the atom of the parameter list, where the associated atom has been derived from.

Informations about a selected bond label

Bond label no.	Defines the zero-based index of the bond label in the bond label list.
Label text	The contents of the bond label.
Label size	The size of the label in Angstroems.
Label position (x, y, z)	The 3D position of the label relative to the center of the associated bond (this is the centerpoint of the two connected atoms).
Bond no.	The zero-based index of the associated bond in the list of created bonds.
Atom symbols	The symbols of the atoms of the parameter list, where the associated atoms has been derived from, which are connected with the associated bond.

Informations about a selected text

User-defined text no.	The zero-based index of the text in the list of user-defined text strings.
Content	The contents of the text string.
Text size	The size of the text in centimeters.
Text position	The position of the leftmost point of the baseline of the text relative to the structure windows's or page's center, in centimeters.

Information about the coordinate system or legend of atom types

If coordinate system or legend of atom types have been selected, the position relative to the reference point in centimeters as well as the reference point itself are given.


Printing, Copying, and Saving the Structure Picture: Overview

This chapter gives you information about printing and forwarding the structure picture to other applications, especially:

- how to define the page format and select the printer,

- how to optimize banding when a rendered picture is to be printed,

- how to print with the usage of the Print dialog,

- how to print directly without using the Print dialog,

- how to use page view and print preview to control the page format,

- how to copy the contents of the structure picture,

- how to save the structure picture as Windows metafile, bitmap, or as VRML file.


Setting the Page Format

The representation of a structure picture on the screen (within the main pane of the structure window) is a little bit different from the repesentation on a printout. Unless you make use of the page view mode, only a (centered) part of the printout page is visible in the drawing area of the structure window. You can use a grid to get the extent of the structure window or page, rsp., in centimeters.

Structure window and page view displaying the printout page for the same structure picture. The upper window displays only the centered part of the entire page.

A page format must be defined for page view, print preview, and printing itself. If you do not define a page format, Diamond uses the page format that is currently defined for the MS Windows standard printer.

To control or change the page format or to select another printer or to change other printer settings, such as resolution, color mixing, etc., choose the Print setup command from the File menu. The contents of the Printer Setup dialog depend on your desktop system as well as on the printer driver. But in most cases, you can choose the page size (for example "A 4") and the orientation ("landscape" or "portrait").

When a structure picture is printed, Diamond normally uses the black-on-white mode, independent if that mode has been activated for the picture on the screen or not. If you want to print a picture with colored or even black background - as it is represented in non-black-on-white mode on the screen -, you must change the Print black on white setting on the Desktop page of the Options dialog (Options command from the Tools menu.)


Banding of Rendered Pictures

When printing a rendered picture, Diamond must buffer the contents of the page in a memory bitmap, which has the same resolution like the printer. For an A4 page (21.7 x 29 cm), a resolution of 300 dpi (dots per inch) and 24 bits per pixel, this requires about 26,340,000 bytes. If there is not enough main memory, MS Windows will occupy some megabytes from your hard disk. The printer driver will need another megabytes to convert the bitmap to printer commands. If your main memory and hard disk resources are getting low, you may have to wait for a rather long time and/or you will receive an error message.

To avoid these problems, Diamond makes use of so-called banding. A band is a part of the complete memory bitmap, which will be sent to the printer driver after rendering. For that reason, the drawing code must be repeated for each band, which will elongate the printing process, but is usually faster than requesting memory from the hard disk (swapping) by the operating system. The default size value for one band is 8,192 kb. You can alter this value in the input field Size of print buffer on the Desktop page of the Options dialog (Options command from the Tools menu). The optimum value depends on the size of the (available) main memory (RAM) of your system and the speed of your main processor (CPU). Smaller values increase the number of drawing operations, whereas higher values may cause swapping and decrease the system performance.

If you do not want banding to be used, enter zero for the size of the print buffer. Then Diamond renders the picture in one single step to the printer.


Printinf Using Print Dialog
Printing Using Print Dialog

The best way to make the first printout in a Diamond session is to use the Print dialog before the printing process is started. The main reason is, that you often don't know really about the current printer selection and page format. The page view or print preview may give you hint for the actual orientation ("landscape" or "portrait") but not for the actual page size and printer selection.

To print with the usage of the Print dialog, choose the Print command from the File menu, or use the "hotkey" Ctrl+P. (Do not use the printer symbol in the standard toolbar!) In the Print dialog, you have the opportunity to select another printer or change further printer settings (page size, format, etc.). Start printing with the OK button.


Printing Direct

If you know the current printer and page settings or if you want to print for the second, third, etc. time during your Diamond session, you can simply choose the [image] button in the standard toolbar. This starts the printout process immediately without calling the Print dialog.


Print Preview and Page View to Control Page Format

Since a structure picture appears quite different between normal mode and page view mode and the normal mode does not represent the whole page, it is recommended to switch to page view mode before printout or to make use of the print preview mode. For details, see "Page View: Overview".


Copying the Contents of the Structure Picture

The contents of the structure window can be copied to the Windows clipboard. For that, assure that the graphics pane has the focus (e.g. click once on the graphics pane) and then either choose the Copy command from the Edit menu, or push the [image] from the standard toolbar, or use the "hotkey" Ctrl+C.

When flat representation is used, Diamond stores both bitmap and metafile format, in rendered representation mode only bitmap format. The bitmap uses the same size and color depth as the structure window. For a metafile, all objects outside the structure window will be clipped, too.

If flat representation is used, the metafile format is the format of choice, since it is scalable and can be used for printouts on high-resolution printers.

If you use rendered representation instead, you should save the structure picture as bitmap instead of copying it. When you save a bitmap, you have the opportunity to select an arbitrary higher resolution than the screen offers.


Saving the Structure Picture as Metafile, Bitmap, or VRML File

You can save the contents of the structure picture in various formats. Please note that you save only the graphics data in that case but no structural informations.

To save the structure picture in a graphics format, assure that the graphics pane has the focus (e.g. click once on the graphics pane) and then choose the Save as command from the File menu, which opens the Save As dialog. In the Save As dialog, choose one of the following graphics formats:

Windows Metafile	This will save the contents of the structure window in a MS Windows Metafile, which usually has the extension .WMF. (Diamond creates no Enhanced Metafiles.) If you are using page view mode instead, the contents of the whole printout page will be copied to the metafile.
Bitmap	This will save the contents of the structure window or of the printout page, rsp., as "Device-Independent Bitmap" (DIB). When you confirm the Save As dialog with OK, you will be prompted for the resolution and the color depth of the bitmap. You can choose a higher resolution than the screen offers (about 100 dpi only) to get better results when you insert the bitmap into a word processing document, for example. The color depth can be 16 bit or 24 bit (per pixel).
VRML	While metafile and bitmap store the graphics in a 2D format, VRML keeps 3D informations of the objects, when it stores the picture in a VRML file, which usually has the extension .WRL. VRML ("Virtual Reality Modeling Language") files can be viewed with a World-Wide Web browser plug-in, for example in Microsoft Internet Explorer and Netscape Navigator.

After you have chosen the output format, adjust the file namem, if necessary, and confirm with the OK button.

The size of a metafile or a VRML file depends on the number of objects used in the structure picture. The size of a bitmap is independent from the number of objects but depends highly on the bitmap size (in inches), the resolution and the color depth. A bitmap file can have up to ten or twenty megabytes.


Data Sheet: Overview

The data sheet displays the contents of the current structure in the secondary pane (data pane). To open the data sheet, choose the Data sheet command from the List submenu of the Display menu. If the secondary pane has not yet been opened, the mouse cursor will change to split mode, that means you can shift the border line between graphics and data pane to adjust the appropriate width for the data sheet.

The following articles will inform you about the contents of the data sheet and how to print and copy the contents of the data sheet.


Data Sheet: Contents

The contents of the data sheet can be divided into five sections:

Bibliographic data	Contains the following data fields (as far as defined): - the common and systematic name, - the structural and analytical formula, - the authors' names, - the title of the structure or of the publication, - the citation, - the mineral name, - the source of compound, - the name of the structure type, - the creation method, - comments.
Crystal data	Contains crystal data and lattice parameters (as far as defined): - the calculated formula sum, - the calculated formula weight, - the crystal system, - the Hermann-Mauguin space group symbol, - the cell parameters that are mandatory for the crystal system, - the cell volume, - the number of formula units per cell, - the calculated and measured density, - the melting point, - the R value(s), - the Pearson symbol, - the formula type, - the Wyckoff sequence.
Atomic parameters	Contains the list of atomic parameters without anisotropic displacement parameters. For each atom the following informations are given: - the atom symbol, - the (formal) oxidation number (as far as defined), - the Wyckoff letter together with the multiplicity, - the site symmetry symbol, - the site occupation factor (as far as defined and not 1), - the coordinates x, y, and z, which are usually given in crystal coordinates, - the isotropic or equivalent displacement parameter (as far as defined). Wyckoff symbol, multiplicity, and site symmetry symbol can be hidden (see below).
Anisotropic displacement parameters	Contains the list of anisotropic displacement parameters, as far as defined. For each set of parameters, the following informations are given: - the atom symbol, - the six anisotropic displacement parameters, as Uij, Bij or beta-ij.
Selected geometric parameters	Contains the measured or imported (CIF) interatomic distances, angles, and torsion angles (as far as defined). Symmetry information is supplied indirectly by using a superscript Roman number at the atom symbol. The list of symmetry operations follows at the bottom of this section.

To enable or disable the sections, click with the right mouse button into the data sheet (or assure that the data sheet has the focus and then use the Windows 95 context menu key) to open the data sheet context menu. From the context menu, choose the Settings command, which opens the Data Sheet Settings dialog. The five sections are represented as the corresponding checkboxes. For the atomic parameter list, you can choose, if Wyckoff symbol/Multiplicity and site symmetry symbol will be displayed or not.


Copying, Saving, and Printing Data from the Data Sheet

Copying the data sheet

You can copy the entire contents of the data sheet or only the selected range as formatted text (Rich Text Format; RTF) to the MS Windows clipboard. This is the easiest way to include (parts of) the data sheet for example in a word processing document, including text formatting (super/subscripts, bold/italics, tabs, etc.). Before you can copy, you must select at least a part of the data sheet. (Only the selected part will be copied!) Then choose the Copy command from the data sheet context menu, or push the [image] button in the standard toolbar, or use the "hotkey" Ctrl+C. Please assure that the data sheet has the focus. Otherwise the structure graphics would be copied instead, if you use the button or the hotkey.

Saving the data sheet

You can save the contents of the data sheet as Rich Text Format file (including formatting) or as Plain Text file (without formatting). Choose the Save data as command from the context menu, which will open the Save File As dialog. Select the file type, the file name, and then choose OK.

Printing and print preview

You can print the entire data sheet or selected pages or the marked area only. Choose the Print data command from the data sheet context menu, which opens the Print dialog, where you can choose the print range (all; some pages; selection), or adjust printer settings. To estimate the extent of the data sheet when printed (especially the number of pages), you may switch to print preview mode by choosing the Print preview command from the File menu or pushing the [image] button in the standard toolbar.


Distances and Angles: Overview

Like the data sheet or the object lists, the list of distances and/or angles is displayed in the secondary pane (data pane) of the structure window. To open the list of distances and/or angles, choose the Distances and angles command from the List submenu of the Display menu. If the secondary pane has not yet been opened, the mouse cursor will change to split mode, that means you can shift the border line between graphics and data pane to adjust the appropriate width for the list of distances and angles.

The following articles will describe

- how to display distances or angles or both, how to select the distance range, how to select the atom types for distance calculation and how to format the list ("List of Distances and Angles"),

- how to measure distances, angles, and torsion angles,

- how to add selected distances or angles to the list of geometric parameters

- and how to copy, save, and print the list of distances or angles.


Distances and Angles: Settings

The list of distances and/or angles is opened either manually by choosing the Distances and angles command from the List submenu of the Display menu or automatically when opening a new structure window and the default setting displays the list of distances and angles in the data pane. When the list is displayed the first time for a structure, the distances (and as far as necessary the angles) will be calculated automatically, using the previous settings for the distance range (the default range is 0 to 2.5 Angstroems), for all atom types of the structure.

You can stop the calculation with the Ctrl+Break key combination. This may be necessary if the preset distance range is rather big (for example up to 5 Angstroems) and the structure has many atoms in the parameter list. You can update the list of distances and/or angles with the Update command from the context menu of the list of distances and/or angles.

Selecting between distances and angles calculation

To change the settings for distances and/or angles calculation, choose the Settings command from the context menu. Diamond can display either distances or angles only or both distances and angles in the list. Select the appropriate setting in the Settings For Distances and Angles dialog from the Display combo box.

Define the distance range in the input fields Distances' range in Angstroems, and the angle range (if angles are to be calculated) in the input fields Angles' range.

Select the atom types for distance (and angle) calculation from the two lists Calculate... By default, all atom types are selected.

Displaying distances only

Although details of the list format will be treated later, the list displays the following informations if only distances are displayed. The example calculates distances up to 2.5 Angstroems, collects identical distances and uses standard uncertainties. (The output has been copied directly from the list without reformatting:)

Ti  1	F   8	1.732(4)	3x

F   1	2.026(5)	3x

Ti  2	F  10	1.720(6)	1x

F   6	1.745(4)	1x

F   1	1.895(4)	1x

F   5	1.914(5)	1x

F   3	1.947(4)	1x

F   2	2.037(5)	1x

Ti  3	F   7	1.708(4)	1x

F   9	1.732(4)	1x

F   4	1.874(5)	1x

F   2	1.891(4)	1x

F   3	1.995(5)	1x

F   5	2.002(4)	1x

Ti  4	F  11	1.742(4)	3x

F   4	2.058(4)	3x

F   1	Ti  2	1.895(4)	1x

Ti  1	2.026(5)	1x

F   2	Ti  3	1.891(5)	1x

Ti  2	2.037(5)	1x

F   3	Ti  2	1.947(4)	1x

Ti  3	1.995(5)	1x

F   4	Ti  3	1.874(5)	1x

Ti  4	2.058(5)	1x

F   5	Ti  2	1.914(5)	1x

Ti  3	2.002(5)	1x

F   6	Ti  2	1.745(4)	1x

F   7	Ti  3	1.708(4)	1x

F   8	Ti  1	1.732(4)	1x

F   9	Ti  3	1.732(4)	1x

F  10	Ti  2	1.720(6)	1x

F  11	Ti  4	1.742(4)	1x

Displaying angles only

Although only angles will be displayed in this mode, you have to specify a distance range. The reason is that Diamonds first calculates distances in any case, and then calculates angles between all atoms within the (coordination) sphere. (The list has been abbreviated.)

Ti  1	F   8	F   8	100.61(15)

< omitted for brevity >

F   1	Ti  2	Ti  1	147.97(21)

F   2	Ti  3	Ti  2	148.78(25)

F   3	Ti  2	Ti  3	151.05(22)

F   4	Ti  3	Ti  4	143.40(24)

F   5	Ti  2	Ti  3	152.72(22)

Displaying both distances and angles

Like for the previous option, Diamond calculates distances first, then angles between all atoms of each (coordination) sphere. For this option, Diamond displays the ligand atoms together with the distances from the central atom. (The list has been abbreviated.)

Ti  1	F   8	1.732(4)	F   8	1.732(4)	100.61(15)

< omitted for brevity >

F   1	Ti  2	1.895(4)	Ti  1	2.026(5)	147.97(21)

F   2	Ti  3	1.891(5)	Ti  2	2.037(5)	148.78(25)

F   3	Ti  2	1.947(4)	Ti  3	1.995(5)	151.05(22)

F   4	Ti  3	1.874(5)	Ti  4	2.058(5)	143.40(24)

F   5	Ti  2	1.914(5)	Ti  3	2.002(5)	152.72(22)

List format

The list format depends mainly on the selected option, that means if distances or angles or both are being displayed. But there is a lot of further settings available from the context menu of the list of distances and/or angles:

Standard uncertainties	Choose the Standard uncertainties command from the context menu, if standard uncertainties shall be calculated and displayed for both distances and angles, or not.
Coordination number	Choose the Coordination number command from the context menu, if Diamond shall collect equal distances to symmetry equivalent atoms. In  this case, the distance value will be listed only once together with the coordination number, e.g. "6x".
Repeat first symbol	Choose the Repeat first symbol command from the context menu, if you want the symbol of the central atom being repeated in every row of the list. This is useful, if you copy the list, e.g. to a spreadsheet. Normally the central atom is not repeated for each line.
Unit	Choose the Unit command from the context menu to select the distance unit from the submenu. Angstroems (default), picometers, and nanometers are available.
Symmetry code	Choose the Symmetry code command from the context menu, if you want to display the symmetry code, the atom code, or no code. The symmetry code is often useful to identify the symmetry operations that generate the atom in the coordination sphere of the central atom. (The central atom has a symmetry code of "x,y,z" in any case.)

The following example compares the usage of coordination numbers (upper part) and symmetry codes in sodium chloride (lower part):

Na1	Cl1	2.810	6x

Cl1	Na1	2.810	6x

Na1	Cl1	x, -0.5+y, -0.5+z	2.810

Cl1	-0.5+x, -1+y, -0.5+z	2.810

Cl1	-0.5+x, y, -0.5+z	2.810

Cl1	-0.5+x, -0.5+y, -1+z	2.810

Cl1	-0.5+x, -0.5+y, z	2.810

Cl1	-1+x, -0.5+y, -0.5+z	2.810

Cl1	Na1	1+x, 0.5+y, 0.5+z	2.810

Na1	0.5+x, y, 0.5+z	2.810

Na1	0.5+x, 1+y, 0.5+z	2.810

Na1	0.5+x, 0.5+y, z	2.810

Na1	0.5+x, 0.5+y, 1+z	2.810

Na1	x, 0.5+y, 0.5+z	2.810


Measuring Distances, Angles, and Torsion Angles

You can interactively measure:

- distances between two atoms each,

- angles between three angles each,

- torsion angles between four angles each.

For that, Diamond uses a special mode, the measure mode, where you click on two, three, or four atoms, rsp. to get the corresponding value. The distances are given in Angstroems, the angles in degrees, both with standard uncertainties, if standard uncertainties are available with the structural parameters. The geometric informations (the value itself and the atoms concerned, including symmetry operations) will be stored with the structure document and can be used, for example, to export them as geometric parameters.

To enter the measure mode for distances, choose the Distances command from the Tools menu, or press the [image] button in the Measure toolbar. The cursor symbol changes to an arrow with a ruler. The Distances window is displayed containing a list of previously measured distances or distance values that have been imported from a CIF (geom_dist_... etc.). New distance values will be appended to the end of the list.

Entering the measure mode for angles and torsion angles is similar: Choose the Angles or Torsion angles command, rsp., from the Tools menu, or press the [image] button or the [image] button, rsp., from the Measure toolbar.

To measure a distance, click with the left mouse button on the two atoms, one after the other. After the second click the distance will be calculated and the information added to the list. If the distance has already been caught, the corresponding row in the list will be selected.

To measure an angle, you must click on three atoms, one after the other. The second atom is the atom at the apex of the angle.

To measure a torsion angle, you must click on four atoms, one after the other. The torsion angle is calculated as described in Klyne, W. & Prelog, V. (1960), Experientia, 16, 521. The vector direction from the second to the third atom is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector from the second to the first atom onto the projection of the vector from the third to the fourth atom. Clockwise torsions are positive, counterclockwise torsions are negative.

Informations about each reported or measured distance

For distances, angles, and torsion angles, the measure window uses different formats. This is the format for distances:

Atom #1	The symbol of the first atom. The symbol comes from the atomic parameter list.
Atom #2	Dito for the second atom.
SymmCode	The symmetry code of the second atom. The symmetry code for the first atom is "x,y,z" in any case.
Dist.	The distance between atom #1 and atom #2 in Angstroems.

Informations about each reported or measured angle

If three atoms #1, #2, and #3 are clicked one after the other, atoms #1 and #3 define the two atoms at the sides of the angle, atom #2 is the atom at the apex.

Atom #1	The symbol of atom #1. The symbol comes from the atomic parameter list.
SymmCode	The symmetry code for atom #1.
Atom #2	The symbol of atom #2. No symmetry code will be given for atom #2, since the symmetry code for this atom is "x,y,z" in any case.
Atom #3	The symbol of atom #3.
SymmCode	The symmetry code for atom #3.
Angle	The angle at atom #2, between the atoms #1 and #3, given in degrees.

Informations about each reported or measured torsion angle

Compare the definition of the torsion angle above.

Atom #1	The symbol of atom #1. The symbol comes from the atomic parameter list.
Atom #2	The symbol of atom #2.
Atom #3	The symbol of atom #3.
Atom #4	The symbol of atom #4.
Angle	The torsion angle, given in degrees.

Editing the list of distances, angles, or torsion angles

To copy the selected rows from the list - for example into a spreadsheet -, push the Copy button in the measure window. To delete one or more distances, angles, or torsion angles, rsp., select the corresponding rows, and push the Delete button.


Adding Selected Distances or Angles to Geometric Parameters

You can add selected distances or angles to the corresponding lists of geometric parameters. The lists of geometric parameters may be a list of measured or imported distances or angles. Since torsion angles are not calculated in the list of distances and angles, they cannot be added to the list of measured torsion angles.

To add one or more distances to the list of measured distances, assure that only distances are displayed in the list, and select the corresponding rows in the list, then choose the Add command from the context menu of the list of distances.

To add one or more angles to the list of measured angles, assure that either the "angles only" or "distances and angles" option is set for the list, then select the corresponding rows in the list, and choose the Add command from the context menu. If the list displays both distances and angles, only the angles are added to the list of measured or reported angles.


Copying, Saving, and Printing the List of Distances or Angles

Copying the list of distances or angles

You can copy the selected rows of the list of distances and/or angles to the Windows clipboard. Each value in a row is separated by a tab from its neighbour, so that you can directly import the copy into a spreadsheet, for example. For that it is recommended that the first atom symbol is repeated in each row. (The default setting displays the atom symbol in the first column only once.) Choose the Repeat first symbol command from the context menu of the list of distances and/or angles. To copy the selected rows, choose the Copy command from the context menu, or push the [image] button in the standard toolbar, or use the "hotkey" Ctrl+C. Please assure that the list of distances and/or angles has the focus. Otherwise the structure graphics would be copied instead, if you use the button or the hotkey.

Saving the list

You can save the entire contents of the list in various text formats:

Text with separators	*.CSV	The contents of the columns of one row are separated by semicolons. Rows are separated by line feeds.
Text with tabs	*.TXT	The contents of the columns of one row are separated by tabs. Rows are separated by line feeds.
Formatted text with spaces	*.PRN	Each column has a fixed number of characters (filled with blanks if necessary). Rows are separated by line feeds.

At least one of the mentioned formats can be imported from the common spreadsheet applications (MS Excel uses all three formats, for example.) To save the list contents, choose the Save list as command from the context menu, which will open the Save File As dialog. Select the file type, the file name, and then choose OK.

Printing and print preview

You can print the entire list or selected pages or the marked rows only. Choose the Print list command from the context menu of the list, which opens the Print dialog, where you can choose the print range (all; some pages; selection), or adjust printer settings. To estimate the extent of the list when printed (especially the number of pages), you may switch to print preview mode by choosing the Print preview command from the File menu or pushing the [image] button in the standard toolbar.


Object Lists: Overview

The secondary pane (or data pane) of the structure window can be used to display several object lists:

- the atomic parameter list including anisotropic displacement parameters,

- the list of created atoms,

- the list of atom types,

- the list of created bonds,

- the list of bond types,

- the list of coordination polyhedra.

To open an object list, choose the List command from the Display menu, and select the corresponding entry from the submenu. If the data pane has not yet been opened, Diamond switches to split mode, where you can define the width of the object list.

For each object list, you can select the columns to be displayed as well as the sort criterion.

The object lists can be used as versatile aid to select atoms, bonds, or polyhedra in the structure picture.


Object Lists: Contents and Settings

To change the format of an object list, choose the List format command from the context menu. To adjust column widths, use the mouse to drag the separators to the left or right. To change the sort order, click on the corresponding header of the column. To invert the sort order, click once again on the header.

List of atomic parameters

The list of atomic parameters may contain the following informations about each atom including its anisotropic displacement parameters:

Parm. no.	The zero-based sequential number of the atom in the parameter list.
Element	The element symbol of the atom including H/D atoms attached with this atom, e.g. "OH2".
Symbol	The symbol used for the atom, e.g. "C11A".
Ox.	The (formal) oxidation number of the atom or blank if not defined.
Mult.	The multiplicity of the atom site.
Wyck.	The Wyckoff letter of the atom site.
X, Y, Z	The x-, y-, and z-coordinate of the atom site, which is usually given in crystal coordinates (fractional coordinates).
Occ.	The site occupation factor for the atom on the site as far as defined and less than one.
B/U iso/equiv	The isotropic or equivalent displacement parameter of type B or U.
B/U/beta 11 etc.	The six anisotropic displacement parameters of type Bij, Uij, or beta-ij.

List of created atoms

The list of created atoms may contain the following informations about each created atom, including pseudo atoms that represent cell corners:

Atom no.	The zero-based sequential number of the atom in the list of created atoms. The lowest number is 4, since the atoms #0 through #3 are reserved to represent the origin and three terminal points of the unit cell axes a, b, and c.
Atom	The symbol of the atom in the parameter list.
Atom code	The atom code of the created atom.
Symmetry	The symmetry of the created atom, e.g. "-1+x, x-y, 0.5+z".
Crystal coordinates	The coordinates of the created atom referring to the crystal coordinate system.
Reference coordinates	The coordinates of the created atom referring to the reference coordinate system.
View coordinates	The coordinates of the created atom referring to the view coordinate system.

List of created bonds

The list of created bonds may contain the following informations about each created bond, including pseudo bonds that represent cell edges:

Bond no.	The zero-based sequential number of the bond in the list of created bonds. The lowest number is 3, since the atoms #0 through #2 are reserved to represent the unit cell axes a, b, and c.
Atom #1	The symbol of the first connected atom in the parameter list.
Atom code #1	The atom code of the first connected atom.
Crystal coordinates #1	The coordinates of the first connected atom referring to the crystal coordinate system.
Atom #2	The symbol of the second connected atom in the parameter list.
Atom code #2	The atom code of the second connected atom.
Crystal coordinates #2	The coordinates of the second connected atom referring to the crystal coordinate system.
Length	The bond length (the distance between the connected atoms #1 and #2), in Angstroems.

List of atom types

The list of atom types may contain the following informations about each atom type of the current structure:

Atom type no.	The zero-based sequential number of the atom type.
Symbol	The atom type symbol, e.g. "Fe+3".
EffRad	The effective atomic or ionic radius, in Angstroems, which is used to calculate bonding spheres.
DrawRad	The drawing radius, in Angstroems, used to display created atoms associated with this atom type in the ball-and-stick model.
SpacFRad	The drawing radius used for the space-filling model, in Angstroems.

List of bond types

The list of bond types may contain the following informations about each bond type (atom type combination) of the current structure:

Bond type no.	The zero-based sequential number of the bond type.
Symbol #1	The atom type symbol of the first atom type of the atom type combination.
Symbol #2	Dito for the second atom type.
Enabled	"yes" if atoms associated with the atom types of this bond type may be connected. Otherwise "no".
RMin	The lower border of the bonding sphere, in Angstroems.
RMax	The upper border of the bonding sphere, in Angstroems.

List of coordination polyhedra

The list of coordination polyhedra may contain the following informations about each coordination polyhedron:

PolyNo	The zero-based sequential number of the coordination polyhedron.
Atom no.	The zero-based sequential number of the central atom in the list of created atoms.
Symbol	The symbol of the central atom from the parameter list.
Ligands	The number of ligand atoms in the coordination sphere of the polyhedron, e.g. six for an octahedron.
Faces	The number of faces (polygons) of the polyhedron, e.g. eight for an octahedron.
RMin	The distance between the central atom and the closest atom in the coordination sphere of the polyhedron, in Angstroems.
RMax	Dito for the atom that is most far away, in Angstroems.


Selecting Atoms, Bonds, or Polyhedra From an Object List

The object lists in the secondary pane of the structure window support the selection of atoms, bonds, and coordination polyhedra in the structure picture. Both the list of created atoms and the list of created bonds represent the created atoms and bonds, rsp., of the structure picture in the graphics pane. Thus if you select an atom (or multiple atoms) in the graphics pane, it will automatically be selected in the atom list, and vice versa. The same is for bonds in the graphics pane and in the bond list. Of course, you can combine selection in the graphics pane with selection in the object list. For example, sort the atoms in the list for atom symbols, then select a range of rows, and finally change some selection in the graphics pane by using extended selection. (Hold down the Shift key and click with the left mouse button to invert the selections of several objects.)

The lists of atomic parameters, atom types, and bond types may assist you when selecting atoms or bonds, rsp., which are associated with selected atoms from the parameter list or atom types or bond types. If you want to select all atoms in the structure picture, which are derived from - for example - the atom with the symbol "P(1)", open the atomic parameter list in the object list and select the atom "P(1)" in this list. Then choose the Select atoms command from the context menu of the list, which will select all atoms in the graphics pane, which are derived from "P(1)". In principle, you can use the same method for the lists of atom types and bond types. From the bond type list, you can select all created bonds associated with the selected bond types.

If you use the list of coordination polyhedra, the central atoms of the selected polyhedra will automatically be selected in the graphics pane, and vice versa.

See also:

Selecting Objects


Orientation: Overview

This chapter informs you about the orientation and the position of the structure within the window or printout page, rsp. You will get to know:

- how to define the center of rotation,

- how to define the orientation and position of the structure,

- how to rotate and shift the structure,

- how to define views along selected axes,

- how to define a view towards a plane given by Miller indexes h,k,l,

- how to make use of the continuous rotation ("Rock and Roll").


Center of Rotation

By default, the center of rotation lies in the common origin of all three coordinate systems (crystal, reference, and view coordinate system), but can be changed manually or automatically. The center of rotation is an important reference point within the structure picture. By default, the center of rotation is projected into the center of the picture (or structure window), but can be shifted later.

Manual setting of the center of rotation

To set the center of rotation to the position of a selected atom, simply select the atom and then push the [image] button in the Display toolbar, or use the "hotkey" Shift+F9. Instead of one single atom you can select multiple atoms and move the center of rotation into the center of the selected atoms. If no atom has been selected, the center of rotation is moved into the center of all atoms.

With the Center of Rotation dialog, you can also set the center of rotation into an arbitrary position (x,y,z) using either crystal or reference coordinates. To open this dialog, choose the Center of rotation command from the Display menu. There you can also decide if cell edges shall be considered, if the center of rotation is to be set into the center of all created atoms.

Automatic centering of the structure

Check the checkbox Automatic centering in the Center of Rotation dialog, if you want the center of rotation be set automatically into the center of all created atoms after each building operation. That means, for example, that the center of rotation moves from the start-up value (0,0,0) to (1/2,1/2,1/2) in crystal coordinates after you have generated the contents of the unit cell, if this option is enabled. This centers the structure picture automatically within the structure window, since the center of rotation is automatically projected into the center of the structure window (unless the reference point has been shifted).


Orientation and Position

The current orientation of the structure is defined by the contents of the orientation matrix. The orientation matrix converts reference coordinates to view coordinates. In the basic orientation, where the orientation matrix is the identity matrix, the x-axis of the reference coordinate system points to the right, the y-axis to the top, and the z-axis towards the viewer.

The current orientation can be described with three rotational angles RX, RY, and RZ. If you start with the basic orientation, you first rotate RX degrees along the x-axis, then RY degrees along the y-axis, and finally RZ degrees along the z-axis to come to the current orientation. (Though there is an infinite number of angle triplets to rotate from the basic to the current orientation.)

The 3D coordinates of the objects cannot be shifted, but the 2D projection of the structure can be shifted horizontally and vertically. This 2D position of the projection of the structure in the 2D drawing area is relative to the center of the drawing area (center of the graphics pane as well as center of the printout page), and is given in centimeters.

Defining orientation and position

To check or define the orientation or the position or both, choose the Orientation command from the Display menu, which opens the Orientation dialog. The current rotational angles in degrees are given in the input fields of the Angles of rotation along ... axes group, whereas the position in centimeters relative to the center of the drawing area is given in the input fields of the Center of rotation... group.

Resetting the orientation

You can reset the orientation to the default orientation. By default, the default orientation is identical with the basic orientation, which means XR = YR = ZR = 0 for the three rotational angles. The default orientation can be changed in the View dialog. See the article "Viewing Along Selected Axes" how to set the default view axis.


Rotating and Shifting the Structure

You can rotate the structure with the mouse, step by step with the keyboard or incrementally by entering angle values. Shifting of the structure within the drawing area is principally done in the same way.

Tracking modes

Diamond offers the so-called tracking mode for rotation as well as shifting. To enter the tracking mode, either push a button in the Tracking toolbar, or use the corresponding command from the context menu of the graphics pane:

Rotation along x/y-axes		Prepares Diamond for rotation along both x- and y-axis.
Rotation along z-axis		Dito, for z-axis.
Shifting		Prepares Diamond for shifting the structure horizontally and vertically.

In the tracking mode, the mouse cursor changes to a symbol made up of arrow plus a symbol signing the mode of operation. In this mode, you cannot select objects. To return to standard selecting mode, either push the [image] button in the Tracking toolbar, or press the Escape key.

The rotation or shifting will not be started before you press down the left mouse button. With the left mouse button down, the structure rotates along selected axes or moves horizontally and vertically, until you release the left mouse button. If you are rotating along x- and y-axis, vertical increments of mouse movement rotate along the x-axis of the view coordinate system, horizontal increments along the y-axis. When rotating along the z-axis, vertical increments of mouse movement rotate the structure along the z-axis. When shifting the structure within the drawing area, the structure's position follows horizontal and vertical shifts of the mouse simultaneously.

You can alter the speed of rotation, that means the amount of rotation relative to mouse movement, as well as the ratio of mouse shift and structure shift on the Tracking page of the Options dialog. To open the Options dialog, choose the Options command from the Tools menu. The current values, which are global for all structure windows, are defined in the input fields Degrees along ...axes per cm mouse movement and Shifting in cm per cm mouse movement, rsp.

By default, the mouse cursor changes to the same symbol that is displayed when entering the tracking mode but without arrow, indicating that you cannot select any menu command or push any toolbar button while you are rotating or shifting the structure. You can hide the mouse cursor during rotation or shifting, rsp. For that, check the checkbox Hide mouse cursor while tracking on the Tracking page of the Options dialog. Thus the cursor cannot reach the window's borders so that you may rotate or shift the structure nearly continuously. Otherwise you cannot continue rotation or shifting, when the mouse cursor has reached the border of the Windows screen, unless you release the left mouse button, move the mouse back to the screen's center and re-enter rotation or shifting mode, rsp.

Stepping

While tracking means simultaneous movement of structure and mouse, stepping stands for stepwise movement of the structure caused by hits on several keys. Each hit on the Cursor up and Cursor down key rotates along the x-axis, whereas each hit on the Cursor left and Cursor right key rotates along the y-axis. To rotate along the z-axis, use the Page up and Page down keys. To shift the structure within the drawing area, hit the cursor keys on the numerous pad.

To change the amounts of rotation or shift for each single keystroke, use the Stepping page of the Options dialog. To open the Options dialog, choose the Options command from the Tools menu. Define the amount of rotation (in degrees) along the x-, y- and z-axis for each single hit on a cursor or PageUp/PageDown key in the input fields X, Y and Z of the input field Degrees along ...axes per keystroke. Define the amount of horizontal and vertical shift for each hit on a cursor key (numerous pad) in the input fields Horizontal and Vertical of the group Shifting in cm per keystroke.

Defining incremental values

To rotate the structure for a arbitrary amounts of degress along selected axes, choose the Rotate command from the Display menu, which opens the Rotate Structure dialog, where you can define the amounts of rotation in degrees for each axis. You can simply repeat the incremental rotation by pushing the Apply button for each increment.

To shift the structure for arbitrary centimeters within the drawing area, choose the Shift command from the Display menu, which opens the Shift Structure dialog, where you can enter the horizontal and vertical amounts of shift in centimeters.


Viewing Along Selected Axes

To define a view along the a, b, or c axis of the unit cell, or along the x, y, or z axis of the reference coordinate system, or along an arbitrary direction, choose the View command from the Display toolbar, which opens the View dialog.

Viewing along an axis

When pushing one of the six pushbuttons a, b, c, x, y or z, the structure will be oriented in this way that the vector a, b or c of the unit cell or the x-, y- or z-axis rsp. of the reference coordinate system points towards you. If the checkbox Opposite direction is checked, the selected axis points away from you instead towards you.

Viewing along a vector defined by uvw

Enter the u, v, and w value into the input fields u, v and w to define a vector pointing from the origin to the point with crystal coordinates (u, v, w). The structure will be oriented according to the currently set uvw values, if the Set button is pushed.

Defining axis

To define a view axis through two selected atoms, push the Define axis button. This closes the View dialog and lets you select two atoms #1 and #2. An axis is defined between these two atoms. The center of rotation will be set into atom #1. The structure will then be oriented in this way that the axis to atom #2 points towards you.

Defining a view as standard orientation

You can define a preferred view as default orientation for new structures or as standard orientation, when the Reset orientation command in the Display menu is called. For that, check the checkbox Save view as standard orientation in the View dialog. If for example the button a is pushed and then this dialog closed, all new structures have the a-axis pointing towards you as default orientation. The Reset orientation command will let the a-axis point towards you, too.


Viewing Towards a Plane Given By Miller Indexes h,k,l

You can choose an orientation where a plane with Miller indexes h, k, and l is projected to the xy-plane of the view coordinate system, that means the plane is parallel with the drawing or printing area.

You can enter values for h, k, and l in the View towards plane group of the View dialog (View command from the Display menu). You may use integer numbers as well as non-integer numbers.

The Miller indexes corresponding to the current orientation are given below the three input fields. When calculating the Miller indexes from the current orientation, Diamond tries to get the nearest integer values for h, k, and l unless no integer value less than 100 can be found for h, k, and l.


Continuous Rotation ("Rock and Roll")

Diamond offers a mode with continuous rotation of the structure along selected axes with arbitrary rotational amounts, which is called "Rock and Roll". ("Rock" because you can also define border values, where the rotational direction is inverted, that means, the structure turns back and forth.)

Switching Rock and Roll on and off

To switch Rock and Roll on or off, using the default settings for rotational amounts and selected axes, push the [image] button in the Tracking toolbar.

Changing the settings

To select the axes for rolling, select an axis for rocking (or no axis for no rocking), and to specify the rotational speeds, choose the Rock'n'Roll command from the Tolls menu, which opens the Rock'n'Roll dialog. Define the rotational speeds referring to the three axes x, y, and z of the view coordinate system in degrees per second in the group Speed of rotation (input fields x-axis, y-axis, z-axis). If multiple axes are selected (that means the corresponding angle in the input field is not zero), the rank order of axes during rotation is x, y, z. If the rotation should change its direction for a selected axis, check the appropriate radio button in the Rocking around axes group, or choose No rocking. The border angles in degrees for rocking can be entered in the two input fields of the group Border angles. If the continuous rotation reaches one of these angle values, the direction of the rotation referring to the axis selected in Rocking around axes is inversed.


Undo command
Undo command (Edit menu)

Cancels the latest change of the "structure document" (building up, deleting or changing of display). The operation to be canceled is displayed after the "Undo:“ item in the Edit menu, unless no Undo is possible (which means the structure document has not been changed).

The Undo operation itself can be canceled too, that means the state before the Undo operation is restored. This is done with the Redo command in the Edit menu.

Remarks

The "Undo" and "Redo" functions refer to the structure in the currently active structure window only! Example: If you first change structure A and then focus the picture of structure B, the "Undo" or "Redo" function applies to structure B ! That means you cannot cancel any changes of structure A as long as structure B is focussed and not until structure A is activated again.

You cannot cancel any changes to a structure after its corresponding structure window has been closed.

Neither closing nor saving of structural data can be cancelled. But you may undo the last operations and then save the restored state.

See also:

Working With Diamond: Undo and Redo


Redo command
Redo command (Edit menu)

Cancels the latest Undo operation, that means returns to the state before the last Undo operation. The operation to be recovered is displayed after "Redo:", unless no Redo is possible.

Remarks

The "Undo" and "Redo" functions refer to the structure in the currently active structure window only! Example: If you first change structure A and then focus the picture of structure B, the "Undo" or "Redo" function applies to structure B ! That means you cannot cancel any changes of structure A as long as structure B is focussed and not until structure A is activated again.

You cannot cancel any changes to a structure after its corresponding structure window has been closed.

Neither closing nor saving of structural data can be cancelled. But you may undo the last operations and then save the restored state.

See also:

Working With Diamond: Undo and Redo


Bibliographic data command
Bibliographic data command (Edit menu)

Opens the Bibliographic data dialog to edit the following data:

•	Structural formula,

•	analytical formula,

•	trivial (common) name,

•	systematic (IUPAC) name,

•	structure type,

•	mineral name,

•	source of compound or origin of the mineral,

•	measured formula weight,

•	measured density,

•	melting point,

•	resdiual factors Rall and Robs,

•	number of formula units per cell (Z),

•	title of publication or some other assigned title,

•	name(s) of the author(s),

•	ASTM Journal Coden, publication year, volume, first and last page,

•	Chemical Abstracts code,

•	origin (crystallographic database),

•	database-specific reference code,

•	recording date and latest update (database),

•	creation method,

•	database-specific remarks,

•	comments.

See also:

Editing bibliographic data


Compound page (Bibliographic data dialog)
Compound

The Compound page is part of the Bibliographic data dialog. Here you can edit textual information about formula, name, and origin of the compound.

Formula (structural)

Defines the structural formula.

Formula (analytical)

Defines the formula sum which describes the analytical composition of the compound.

Name (common)

Defines the trivial name of the compound.

Name (systematic)

Defines the systematic name of the compound.

Structure type

Defines the structure type.

Mineral name

Defines the mineral name of the compound.

Compound source

Defines the origin of the compound.

Remarks:

All text fields except the formula fields may contain special text formatting characters for Greek letters as well as for superscript and subscript. Superscript and subscript are used in the data sheet as well as text fields in the structure picture. Since indices in the formulae are subscripted automatically in the data sheet, these text fields should contain no formatting characters.

See also:

Editing bibliographic data


Crystal data page (Bibliographic data dialog)
Crystal data

The Crystal data page is part of the Bibliographic data dialog.

Formula weight

The formula mass in daltons measured by a non-diffraction experiment. Do not mismatch this value with the calculated formula weight, which appears in the Crystal Data section in the data sheet, and which is calculated automatically by Diamond.

Density (measured; g/cm³)

The measured density in grams per cubic centimeter, measured using standard chemical and physical methods. Do not mismatch this value with the calculated density, which appears in the Crystal Data section in the data sheet, and which is calculated automatically by Diamond.

Melting point (K)

The melting point in Kelvin.

R (all)

The residual factor ("R value") for all reflection data.

R (obs)

The residual factor for reflection data classified as "observed".

Number of formula units per cell (Z)

The number of formula units per cell, the so-called "Z value". This must be an integer number.

Remarks

None of the data mentioned above are mandatory for Diamond. Since the number of formula units (Z) is used by Diamond to calculate formula sum, formula weight, and density for the Crystal Data section of the data sheet, Diamond assumes a value of 1, if no Z value is given here.

See also:

Editing bibliographic data


Publication page (Bibliographic data dialog)
Publication

The Publication page is part of the Bibliographic data dialog.

Title

Defines the title assigned to the crystal structure or - if the data come from a publication - the title of the publication.

Authors' names

Defines the name(s) of the author(s). Multiple names are separated by commas. The sur-name should precede the intial(s) of the first name(s), e.g. "Smith R F, Miller K, Roberts A“.

Journal

The journal where the crystal structure was published. Coden defines the ASTM Journal Coden of the journal, Year the year of publication, Volume the volume number, and Pages the number of the first and last page rsp. of the publication.

Chemical Abstracts Code

The Chemical Abstracts Code.

See also:

Editing bibliographic data


Origin page (Bibliographic data dialog)
Origin

The Origin page is part of the Bibliographic data dialog.

Database

The original database of the compound. DIAMOND distinguishes between:

- the Inorganic Crystal Structure Database (ICSD),

- the Metals Data File (CRYSTMET),

- the Cambridge Structural Database (CSD),

- the Protein Data Bank (PDB).

Other or unknown database should be set if the database is unknown or the compound's origin is no database.

Reference code

The database-specific code of the compound (e.g. ICSD Collection Code, CSD Reference Code etc.).

Recording date

The date when the compound was recorded in the database.

Last update

The latest date when the compound was updated in the database.

Creation method

A description how data was entered or created into the original form.

Remarks

Database-specific remarks. These remarks can consist of multiple lines. Use the Enter key to begin a new line. (Enter does not close the dialog.)

See also:

Editing bibliographic data


Comments page (Bibliographic data dialog)
Comments

The Comments page is part of the Bibliographic data dialog.

Comments

Comments about the compound. This text may consist of multiple lines. Use the Enter key to begin a new line. (Enter does not close the dialog.) For tabstops you must use Ctrl+Tab instead of Tab only, else this input field would loose focus.

See also:

Editing bibliographic data


Symmetry command
Symmetry command (Edit menu)

Opens the Symmetry dialog where you can enter or select a space group.

See also:

Editing space group


Cell command
Cell command (Edit menu)

Opens the Cell parameters dialog where you can edit the cell parameters a, b, c, alpha, beta, and gamma.

See also:

Editing cell parameters


Symmetry dialog
Symmetry

Defines the space group for the compound.

Hermann-Mauguin symbol

The Hermann-Mauguin space group symbol and (in parentheses) the space group number according to the International Tables of Crystallography (IT).

The next field contains a list of all space group settings stored in the Diamond space group file. This list appears as tree view (like the directory view in the MS Windows 95/NT Explorer). For each space group, the first setting according to IT is listed. Further settings can be obtained by opening the corresponding node in the tree view, which is marked with a plus (+) sign. The node can be closed by clicking on the minus (-) sign. Nodes can also be opened and closed with the Cursor Right and Cursor Left key rsp.

The current selection in the tree view is automatically copied to the Hermann-Mauguin symbol input field.

Sort alphabetically

Normally the space groups in the tree view are sorted for increasing space group numbers according to IT (1 through 230). If this checkbox is checked, the space groups are sorted alphabetically in increasing order of the first settings according to IT. Further settings for a space group will be sorted in the same way if the corresponding node has been opened.

The text field on the right displays informations about the currently selected space group:

Internal Space Group Number	The space group number which is handled internally by Diamond to distinguish between different settings of a space group. The first setting according to International Tables of Crystallography (IT) is: IT number * 100 (e.g. 1400 for P 1 21/c 1). Further settings are numbered with IT number*100+1, +2 etc. (e.g. 1401 for P 1 21/n 1; 1402 for P 1 21/a 1 etc.). Special settings from ICSD are numbered 2400, 2500 etc.
Int. Tables or Equivalent No.	The space group number according to IT, this has a range of 1 through 230.
Hermann-Mauguin Symbol	The full form of the Hermann-Mauguin symbol from IT or the ICSD notation (e.g. P121/C1S)
Hall Symbol	The Hall space group symbol according to: Hall, S. R. (1981). Acta Cryst. A37, 517-525.
Schoenflies Symbol	The Schoenflies symbol from IT
Point Group	The short symbol for the point group which the space group belongs to
Laue Group	The symbol of the Laue class
Crystal System	The crystal system
Centrosymmetric	Indicates the presence or absence of centrosymmetry
Centering	The centering
Monoclinic axis	The unique axis if the crystal system is monoclinic
Monoclinic Cell Choice	The number of cell choice in IT
Monoclinic Setting	The monoclinic setting, e.g. "c-ba" for A 1 2/a 1 (no. 15)
Symmetry Matrices	The coordinate triplets of the symmetry matrices of the space group including sequential number
Positions	The positions with multiplicity and Wyckoff letter of the sites, beginning with the general site, and the coordinate triplet of the first symmetry matrix of the general/special site.

This is an example for space group P 1 21/c 1 (no. 14):

Internal Space Group Number:	1400
Int.Tables or Equivalent No.:	14
Hermann-Mauguin Symbol:	P 1 21/c 1
Hall Symbol:	-P_2ybc
Schoenflies Symbol:	C2h^5
Point Group:	2/m
Laue Group:	2/m
Crystal System:	Monoclinic
Centrosymmetric:	yes
Centering:	Primitive (P)
Monoclinic axis:	b
Monoclinic Cell Choice:	1
Monoclinic Setting:	abc
Symmetry Matrices:
(1)	x, y, z
(2)	-x, 0.5+y, 0.5-z
(3)	-x, -y, -z
(4)	x, 0.5-y, 0.5+z
Positions:
4e	x, y, z
2d	0.5, 0, 0.5
2c	0, 0, 0.5
2b	0.5, 0, 0
2a	0, 0, 0

Remarks

There are different ways to define the space group:

The easiest way is to enter the Hermann-Mauguin symbol into the input field Hermann-Mauguin symbol, and then confirm with OK. If the space group symbol is invalid, you will get an error message. For more information how to type a correct space group symbol (e.g. "Fm-3m" or "Fm3-m" or "F m -3 m" etc.), see the article Editing the space group in the online manual. You can control the correctness of the space group symbol by pressing the Tab key after you have typed the symbol in the Hermann-Mauguin symbol input field. This will set the focus to the corresponding entry in the list and display informations in the info field.

Another way is to select the space group (setting) from the tree list below the Hermann-Mauguin symbol input field, check the informations in the right text field, and then confirm with OK.

See also:

Editing space group


Cell parameters dialog
Cell parameters

Defines the cell parameters a, b, c, alpha, beta, and gamma.

a, b, c

Define the cell parameters a, b, and c rsp. These values must be given in Angstroem. Standard deviations may be used.

alpha, beta, gamma

Define the cell parameters alpha, beta, and gamma rsp. These values must be given in degrees. Standard deviations may be used.

Restrict cell parameters to crystal system

If this checkbox is checked, only the mandatory cell parameters according to the crystal system of the actually defined space group are available for editing.

Remarks

After closing the dialog with OK, Diamond checks the six cell parameters, if they fit the crystal system of the actual space group. For example, if you have entered a value for b which is different from a for a cubic cell (which is not possible, if the checkbox Restrict cell parameters to crystal system has been checked), you will be asked to change the space group.

If a structure picture already exists, Diamond recalculates the coordinates of all created atoms. The connectivity will not be affected, but it is recommended to check the bond spheres, since the interatomic distances have changed due to the change of cell parameters.

See also:

Editing cell parameters


Atomic parameters command
Atomic parameters command (Edit menu)

Opens the Atomic parameters dialog where you can edit the list of atomic parameters including displacement parameters.

See also:

Editing atomic parameters


Definition page (Atomic parameters dialog)
Definition

The Definition page is part of the Atomic parameters dialog.

Atomic parameters

List of all previously defined atoms in the parameter list. The following brief information is given for each atom:

(1) 	Element symbol;

(2) 	Atom symbol;

(3) 	Oxidation number or "..." if not defined;

(4) 	Multiplicity and Wyckoff letter of the site.

Insert

Inserts a new atom into the parameter list above the actually highlighted atom. See Remarks.

Append

Adds a new atom to the parameter list. The new atom is appended to the end of the parameter list. See Remarks.

Copy from actual atom

If this checkbox is checked, Diamond will create a copy of the actually marked atom. If it is not checked, all fields of the new atom will be undefined. See Remarks.

Delete

Deletes the actually marked atom from the parameter list.

Restore

Restores the previously deleted atom.

Element

Defines the element for the actually marked atom. The element may be typed or selected from the list. The element symbols D and T are used for the H isotopes deuterium and tritium rsp. "?" defines a dummy atom. See Remarks.

Symbol

Defines the symbol for the actually marked atom. The symbol is a string with a maximum of seven characters to describe the atom site. Usually these symbols consist of the element symbol and further identifying characters appended to distinguish this site from other sites with the same atom type, e.g. "Fe 2", "Fe(2)".

Oxidation number

Defines the oxidation number or charge for the actually marked atom. Floating point numbers can be used to determine fractal oxidation numbers. The range is -4.0 to +8.0. If the oxidation number is undefined, enter '*', '?' or leave this field blank.

S. O. F.

Defines the site occupation factor for the actually marked atom. This value has a valid range of greater than 0.0 and less or equal 1.0. If site occupation is not known, enter '*', '?' or leave this field blank.

Attached H/D's

Defines the number of hydrogen atoms attached to the actually marked atom, but not given explicitely in the parameter list. Different nuclides of attached hydrogen atoms cannot be distinguished here.

Description

This field can be used to define a text that describes the actually marked atom. There are no restrictions to the length of this text.

Position

Defines the Wyckoff symbol of the actually marked atom. This symbol consists of the multiplicity (range 1 to 192) and a letter indicating the special or general site (with no blank between). The alpha site of space group P212121 is given as '@'. If neither multiplicity nor letter are known, enter '*', '?' or leave the field blank. If only multiplicity or letter are given, enter the number or the letter only, e.g. '4' (or '4*'), 'a', etc. You can also select one of the Wyckoff symbols which are available for the space group which is actually defined for the compound. See Remarks.

X, Y, Z

Define the crystal coordinates of the site (fractal coordinates x/a, y/b, z/c). Standard deviations may be given, e.g. "0.1234(12)". Fractions (e.g. "1/2") may be given for special sites.

Site

A standard code to signal if the site of the actually marked atoms has been determined by diffraction data or calculated from the geometry of surrounding sites, or has been assigend dummy coordinates:

measured	determined from diffraction measurements
calculated	calculated from molecular geometry
dummy	dummy site with meaningless coordinates

Remarks

There are several options to add atoms to the parameter list:

Append adds an atom to the end of the parameter list, whereas Insert inserts the new atom before the actually marked atom.

For a new atom, all fields will be undefined, unless the checkbox Copy from actual atom has been checked. In the latter case, Diamond makes a copy of all settings of the actually marked atom.

The actually marked atom can be deleted with Delete. Since Diamond stores the parameters for the last deleted atom, this atom can be restored with Restore. Please note that only the last atom can be restored, if you have deleted multiple atoms.

The following parameters of an atom are mandatory:

(a) If the atom site has valid coordinates (determined by diffraction or calculated), X, Y, and Z are mandatory. If the site is no dummy site (see below), a valid element symbol must also be given in Element. Oxidation number, site occupation factor, number of attached hydrogens are not necessary to be given. The Wyckoff symbol will be calculated automatically by Diamond when the dialog is closed with OK.

(b) If the position of the atom has not been determined, leave X, Y, and Z blank. In most cases this "atom" describes H atoms which have not been localized in the unit cell. In such cases the site occupation S.O.F. may exceed 1. If e.g. S.O.F. is 5 and the multiplicity in Position is 4 (usually given as "4*"), there are 20 atoms in the unit cell with no positional parameters.

The element of the actual site (and thus the ordinal number) is defined by Element. A dummy atom, i.e. an atom with well-defined site but without chemical meaning, may be defined by entering a '*' into the input field Element symbol (or leaving it blank). Dummy atoms represent a special kind of atom type. A dummy atom is useful to define coordination polyhedra with no central atom.

Position has a list of all Wyckoff positions of the current space group. If you select a (new) position and then use the Tab key to set the input focus to the next control (that is X) or click on the X input field, the coordinates of this (new) site will automatically be set into the input fields X, Y, and Z rsp., e.g. (x = 0; y = 1/2; z = z). (In this case you must change the "z" to a number afterwards.) This does not work vice versa. That means, if you specify coordinates of a special site, Diamond does not automatically select the appropriate Wyckoff position in Position. (But this does not matter, since Diamond calculates all Wyckoff positions after closing the dialog with OK.)

The order of the atoms in the parameter list can be changed by dragging the actually marked atom to the desired position.

See the article Editing atomic parameters in the online user manual what happens to an existing structure picture on changes in the atomic parameter list.

See also:

Editing atomic parameters


Displacement page (Atomic parameters dialog)
Displacement

The Displacement page is part of the Atomic parameters dialog.

Atomic parameters

List of all previously defined atoms in the parameter list. The following brief information is given for each atom:

(1) 	Element symbol;

(2) 	Atom symbol;

(3) 	Oxidation number or "..." if not defined;

(4) 	Multiplicity and Wyckoff letter of the site.

Insert

Inserts a new atom into the parameter list above the actually highlighted atom. See Remarks.

Append

Adds a new atom to the parameter list. The new atom is appended to the end of the parameter list. See Remarks.

Copy from actual atom

If this checkbox is checked, Diamond will create a copy of the actually marked atom. If it is not checked, all fields of the new atom will be undefined. See Remarks.

Delete

Deletes the actually marked atom from the parameter list.

Restore

Restores the previously deleted atom.

Type

Defines the type of displacement parameters for the actually marked atom:

No displacement parameter(s) defined:	Neither isotropic nor anisotropic displacement parameters are defined
U (anisotropic):	The six values in the Anisotropic parameters input fields are U11, U22, ..., U23.
B (anisotropic):	dito for B11, B22, ..., B23
Beta (anisotropic):	dito for beta11, beta22, ..., beta23
U (isotropic):	The value in Isotropic or equivalent parameter is the isotropic displacement parameter of type U
B (isotropic):	dito for B
anisotropic, unknown type:	The six values in the Anisotropic parameters input fields are anisotropic displacement parameters but not of type U, B, or beta
isotropic, unknown type:	The value in Isotropic or equivalent parameter is an isotropic displacement parameter but of unknown type

Isotropic or equivalent parameter

Defines the isotropic or equivalent displacement parameter of the actually marked atom. Standard deviations may be used. See remarks.

Anisotropic parameters

The six input fields (1,1) through (2,3) define the six anisotropic displacement parameters. Standard deviations may be used.

Remarks

If anisotropic displacement parameters have been defined for the actually marked atom, the value in Isotropic or equivalent parameter describes the equivalent displacement parameter, which should have been calculated according to: Fischer, R. X. & Tillmanns, E. (1988). Acta Cryst. C44, 775-776.This value has probably been imported from a CIF file (data item _atom_site_U_iso_or_equiv or _atom_site_B_iso_or_equiv), and cannot be changed. Diamond does not calculate equivalent displacement parameters from anisotropic displacement parameters.

Anisotropic displacement parameters will not be displayed as thermal ellipsoids unless you have enabled their display using the Thermal ellipsoids command in the Objects menu.

See also:

Editing atomic parameters

Thermal ellipsoids


Atom types command
Atom types command (Edit menu)

Opens the Atom types dialog where you can edit properties of atom types such as design, radii, description etc.

See also:

About Atoms, Atom Types, Bonds, and Bond Types: Atom Types


Definition page (Atom types dialog)
Definition

The Definition page is part of the Atom types dialog.

Atom types

List of all atom types of the compound.

New

Creates a new atom type as copy of the actually marked atom type. This atom type has the same chemical composition, design, radii etc. To distinguish it from the original atom type, an 'A' has been appended to the original symbol. See remarks.

Rendered

If this checkbox is checked, the actually marked atom type will be displayed in rendered representation in the preview window. Otherwise it will be displayed flat without any shading.

Update atoms

If this checkbox is checked, all previously atoms of the structure picture will get the (new) atom type designs. See remarks.

Update resources

If this checkbox is checked, the settings of the atom types of the current compound will be saved in the resources section of the Diamond configuration file.

Reset all

Restores the settings of all atom types of the current compound to those defined in the resources section of the Diamond configuration file.

Symbol

Defines the symbol for the actually marked atom type. This symbol has been generated automatically by Diamond and consists of the element symbol only or the element symbol plus oxidation number (as far as defined). If the atom type describes atoms on mixed sites, all elements of the mixed site are given. This symbol may be changed anyway.

Assign to

Opens the Assign atom type dialog to assign the actually marked atom type to one or more atoms of the parameter list. This is useful, if a new atom type has been defined and to override the automatic assignment of atom types by Diamond.

Description

Describes the actually marked atom type. This can be any free text without limitations in length.

Colors for mixed site representation

If the actually marked atom type describes a mixed site, the colors for the different elements, which are listed in Component, on this type of site are defined in Color. This group does not appear, if the atom type does not describe a mixed site. For more information how to assign colors for mixed site representation, see the article "Definition of Colors for Mixed Site Representation".

Remarks

New together with Assign to can be used to define a new atom type and thus to override the automatic assignment of atom types to atoms from the parameter list. See the article "Assigning a New Atom Type at Runtime" how to define a new atom type.

Changes in the atom type definitions, especially designs, do not necessarily affect the designs of the atoms of a structure picture, unless the checkbox Update atoms has been checked. For more information, see the article "Designing Atoms and Atom Types: Overview" in the online manual.


Design page (Atom types/Edit atoms dialog)
Design

The Design page is part of the Atom type dialog and of the Edit atoms dialog. It is used both for editing the actually marked atom type of the selected atom(s), rsp.

Atom types [Atom type dialog only]

List of all atom types of the compound.

New [Atom type dialog only]

Creates a new atom type as copy of the actually marked atom type. This atom type has the same chemical composition, design, radii etc. To distinguish it from the original atom type, an 'A' has been appended to the original symbol. See remarks.

Rendered

If this checkbox is checked, the actually marked atom type or the selected atom(s), rsp., will be displayed in rendered representation in the preview window. Otherwise it will be displayed flat without any shading.

Update atoms [Atom type dialog only]

If this checkbox is checked, all previously atoms of the structure picture will get the (new) atom type designs. See remarks.

Update resources [Atom type dialog only]

If this checkbox is checked, the settings of the atom types of the current compound will be saved in the resources section of the Diamond configuration file.

Reset all [Atom type dialog only]

Restores the settings of all atom types of the current compound to those defined in the resources section of the Diamond configuration file.

Style

Describes the style of the atom (type). There are different styles available, most of them similar to those used by ORTEP. See remarks.

Unify [Atom type dialog only]

Opens the Unify atom designs dialog to unify selected settings of all atom types with the settings of the actually marked atom type.

Interior

Defines the interior color and "brush" of the atom (type) . See remarks.

Edge

Defines the color, "pen" and thickness of the edge of the atom (type). See remarks.

Pattern

Defines the color and thickness for the drawings inside the atom (type). See remarks.

Remarks

[Atom type dialog only:] New together with Assign to can be used to define a new atom type and thus to override the automatic assignment of atom types to atoms from the parameter list. See the article "Assigning a New Atom Type at Runtime" how to define a new atom type.

[Atom type dialog only:] Changes in the atom type definitions, especially designs, do not necessarily affect the designs of the atoms of a structure picture, unless the checkbox Update atoms has been checked. For more information, see the article "Designing Atoms and Atom Types: Overview" in the online manual.

Colors can be defined separately for the interior, for the edge and for a pattern (as far as defined) of an atom or atom type. Additionally different styles for edges, hatching etc. are available. For a detailed description of atom (type) designs, see the article "Designing Atoms and Atom Types: Overview" in the online manual.


Radii page (Atom types/Edit atoms dialog)
Radii

The Radii page is part of the Atom type dialog and the Edit atom(s) dialog.

Atom types [Atom type dialog only]

List of all atom types of the compound.

New [Atom type dialog only]

Creates a new atom type as copy of the actually marked atom type. This atom type has the same chemical composition, design, radii etc. To distinguish it from the original atom type, an 'A' has been appended to the original symbol. See remarks.

Rendered

If this checkbox is checked, the actually marked atom type or the selected atom(s), rsp., will be displayed in rendered representation in the preview window. Otherwise it will be displayed flat without any shading.

Update atoms [Atom type dialog only]

If this checkbox is checked, all previously atoms of the structure picture will get the (new) atom type designs. See remarks.

Update resources [Atom type dialog only]

If this checkbox is checked, the settings of the atom types of the current compound will be saved in the resources section of the Diamond configuration file.

Reset all [Atom type dialog only]

Restores the settings of all atom types of the current compound to those defined in the resources section of the Diamond configuration file.

Drawing radius [...]

Defines the radius in Angstroem which is used to display the atom or an atom basing upon this atom type in the ball-and-stick model. This radius may be multiplied with several additional factors:

(a) The "overall radius factor", that is used to enlarge or decrease all atoms in the same way, and which is usually 1.0. The overall radius factor can be set in the Display structure dialog, which is opened from the Display command in the Structure menu.

(b) The "ligand atoms reducing factor", that is used to decrease the size of atoms on corners of coordination polyhedra. This value can be set in the Global settings for polyhedra dialog, which can be opened from the Edit polyhedra dialog. The latter dialog is opened from the Edit polyhedra command in the context menu of a polyhedron's central atom.

No ellipsoid representation

If this checkbox is checked, the marked atom(s) or the actually marked atom type will not be displayed as thermal ellipsoid, even if displacement parameters are defined for these atoms/for this atom type and the display of ellipsoids has been enabled. See the article "Exclude Selected Atom Types From Ellipsoid Representation" in the online user manual.

Drawing radius for Space-filling model

Defines the radius in Angstroem which is used to display the atom or an atom basing upon this atom type in the space-filling model.

Effective radius (for bonding spheres) [Atom type dialog only]

Defines the effective radius for the actually marked atom type in Angstroem. This value is used by Diamond to calculate bonding spheres. See the article "Connectivity" in the online user manual.

Remarks

[Atom type dialog only:] New together with Assign to can be used to define a new atom type and thus to override the automatic assignment of atom types to atoms from the parameter list. See the article "Assigning a New Atom Type at Runtime" how to define a new atom type.

[Atom type dialog only:] Changes in the atom type definitions, especially designs, do not necessarily affect the designs of the atoms of a structure picture, unless the checkbox Update atoms has been checked. For more information, see the article "Designing Atom Types".


Material page (used in several dialogs)
Material

The Material page defines material properties of atoms, bonds, and polyhedron faces. It is part of several dialogs:

•	the Atom type dialog

•	the Edit atom(s) dialog

•	the Bond type dialog

•	the Edit bond(s) dialog

•	the Edit polyhedra dialog

•	the Design for new polyhedra dialog

Specular reflectivity

Define the red, green, and blue component of the specular reflectivity.

Emissive reflectivity

Define the red, green, and blue component of the emissive reflectivity.

Shininess

Defines the shininess.

Transparency

Defines the transparency.

Remarks

To get familiar with the above mentioned terms, you should read the article "Designing Atoms and Atom Types: Material Properties" and "Designing Bonds and Bond Types: Material Properties" in the online manual.


Bond types command
Bond types command (Edit menu)

Opens the Bond types dialog where you can edit properties of bond types such as design, radii, description etc.

See also:

About Atoms, Atom Types, Bonds, and Bond Types: Bond Types

About Atoms, Atom Types, Bonds, and Bond Types: Connectivity


Definition page (Bond types dialog)
Definition

The Definition page is part of the Bond types dialog.

Atom type pairs

The list of all bond types, that means all N * (N + 1) / 2 combinations of the N atom types of the compound.

Rendered

Displays the bond in the preview window in rendered form. Otherwise the bond is displayed flat.

Save as default

Saves the design of the actually marked bond type as default design for bonds. This default design is stored in the Diamond configuration file, and will be used as standard bond design for new or imported structures.

Update created bonds

If this checkbox is checked, the designs of all bonds in the structure picture will be updated according to the new settings in the bond type list. Otherwise the designs of the existing bonds will be left unchanged, but bonds created afterwards will get the new designs.

Reset all

Resets all bond type designs to the standard bond design, which is defined in the Diamond configuration file.

Description

Describes the actually marked bond type (free text). There are no restrictions to the text length.

Bonding sphere

If the checkbox Enable bonding within the given range is checked, atoms belonging to the actual atom type combination (bond type) may be connected with bonds, if the distance lies within the given range Lower bound and Upper bound in Angstroem, and one of the bond creating functions is called (e.g. Connect atoms in the Structure menu).

Remark

It is recommended to use the Connectivity dialog to define bonding spheres. To open the Connectivity dialog, use the Connectivity command in the Structure menu.

See also:

About Atoms, Atom Types, Bonds, and Bond Types: Bond Types

About Atoms, Atom Types, Bonds, and Bond Types: Connectivity


Design page (Bond types/Edit bonds dialog)
Design

The Design dialog is part of the Bond types dialog and of the Edit bonds dialog.

Atom type pairs [Bond types dialog only]

The list of all bond types, that means all N * (N + 1) / 2 combinations of the N atom types of the compound.

Rendered

Displays the bond in the preview window in rendered form. Otherwise the bond is displayed flat.

Save as default [Bond types dialog only]

Saves the design of the actually marked bond type as default design for bonds. This default design is stored in the Diamond configuration file, and will be used as standard bond design for new or imported structures.

Update created bonds [Bond types dialog only]

If this checkbox is checked, the designs of all bonds in the structure picture will be updated according to the new settings in the bond type list. Otherwise the designs of the existing bonds will be left unchanged, but bonds created afterwards will get the new designs.

Reset all [Bond types dialog only]

Resets all bond type designs to the standard bond design, which is defined in the Diamond configuration file.

Style

Defines the actually marked bond type or the selected bond(s) to be thin, thick or invisible.

Radius

Defines the radius of the bond in Angstroem, if the bond has the style "Thick".

Fragmentation

If this value is greater than zero, the bond will be drawn fragmentated.

Interior

Defines color and "brush" used for the interior of the bond, if the bond has the style "Thick". If the bond is thin, the brush will not be used, and the interior color will be used as the only color of the thin bond.

Edge

Defines color, "pen", and thickness of the edge of a thick bond. If the bond style is "Thin", no edge color will be used, since a thin bond has no edge.

Remark

For a detailed description of bond (type) designs, see the article "Designing Bonds and Bond Types: Overview" in the online manual.

See also:

About Atoms, Atom Types, Bonds, and Bond Types: Bond Types


Assign atom type dialog
Assign atom type

Assigns atom types to atoms of the parameter list.

Assign atom type...

List of all atom types of the compound. When the dialog has been opened, the atom type is selected, that has been marked in the Atom type dialog.

...to atom(s) from parameter list

List of all atoms in the parameter list. The atoms that are currently assigned to the atom type in the above list are highlighted. The symbol of the atom type, which the selected atoms in the parameter list are assigned to, is given at the right end above this list. "Not unique..." is indicated, if atoms are selected, which do not belong to one and the same atom type.

Assign

Assigns the atom type, which is actually selected in the list Assign atom type..., to all atoms, which are actually selected in the list ...to atom(s) from parameter list.

Remark

Usually this dialog is used to assign a new atom type, which has previously been derived from another atom type in the Atom types dialog. See the article "Assigning a New Atom Type at Runtime" in the online manual.


Unify atom designs dialog
Unify atom designs

This dialog is used to assign several properties of the actual design in the Atom types dialog to all atom types.

Style

If this checkbox is checked, all atom types will get the same style as the actual style.

Interior, Color

Dito for the color that is used to fill atoms.

Interior, Brush

Dito for the brush that is used to fill atoms.

Edge, Color

Dito for the color that is used to draw the edge of the atoms

Edge, Pen

Dito for the pen that is used to draw the edge of the atoms.

Edge, Thickness

If this checkbox is checked, the edges of all atom types will get the same thickness.

Pattern, Color

If this checkbox is checked, the patterns of all atom types will get the same color.

Pattern, Thickness

If this checkbox is checked, the patterns of all atom types will get the same thickness.

See also:

Assigning Selected Properties to All Atom Types


Unify bond designs dialog
Unify bond designs

This dialog is used to assign several properties of the actual design in the Bond types dialog to all bond types.

Style

If this checkbox is checked, all bond types will get the same style as the actual style.

Interior, Color

Dito for the color that is used to fill thick bonds or to draw thin bond lines.

Interior, Brush

Dito for the brush that is used to fill thick bonds.

Edge, Color

Dito for the color that is used to draw the edge of thick bonds.

Edge, Pen

Dito for the pen that is used to draw the edge of thick bonds.

Edge, Thickness

If this checkbox is checked, the edges of all thick bonds or the lines of all thin bonds will get the same thickness.

Radius

If this checkbox is checked, all bond types will get the same radius (used only for thick bonds).

Fragmentation

If this checkbox is checked, all bond types will get the same fragmentation.

See also:

Assigning Selected Properties to All Bond Types


Select all command
Select all command (Edit menu)

This command is used to select objects in the structure picture pane as well as in several lists (secondary pane).

Select all command in the structure picture pane

Resets all selections, then selects all objects of the current structure picture:

•	all atoms (including coordination polyhedra),

•	all bonds,

•	all cell corners,

•	all atom labels,

•	all bond labels,

•	all user-defined texts

Coordinate system and legend of atom types will not be selected.

Select all command in object lists or list of distances and angles

Selects all lines of the object list or of the list of distances and angles, rsp.

Select all command in data sheet

Select the entire text in the data sheet.

See also:

Working With Diamond: Selecting Objects


Invert selection command
Invert selection command (Edit menu)

This command is used to select objects in the structure picture pane as well as in several lists (secondary pane).

Invert selection command in the structure picture pane

1. Resets the selection of all previously selected objects.

2. Selects all objects which have not previously been selected.

Coordinate system and legend of atom types will not be selected.

Invert selection command in object lists or list of distances and angles

1. Resets the selection of all previously selected lines in the object list or in the list of distances and angles, rsp.

2. Selects all lines of the list.

See also:

Working With Diamond: Selecting Objects


Select moleculs command
Select molecule command (Edit menu)

Selects the molecule which the selected atom(s) belong(s) to. Resets all previous atom selection.

See also:

Working With Diamond: Selecting Objects


Filter command
Filter command (Structure menu)

Opens the Filter dialog which enables the selection of certain atoms of the parameter list as well as of special symmetry operators and Bravais translations for building operations.

Remark

Usually this function is used for the investigation of sublattices. To remind the user that a part of the structural data is suppressed, a triangle appears in the lower left corner of the structure window. (This triangle will not be printed.)

See also:

Filter: Overview


Filter dialog
Filter

Enables the selection of certain atoms of the parameter list as well as of special symmetry operators and Bravais translations for building operations.

Atom types

List of all atom types of the current compound. See remark.

Atoms from parameter list

List of all atoms in the parameter list.

Mark all

Selects all atoms of the parameter list (and thus all items in the Atom types list).

Unmark all

Resets all selections in the atomic parameter list (and thus all items in the Atom types list).

Symmetry operations

List of all symmetry matrices in the same sequential order as defined in the Diamond space group info file for the current space group.

Bravais translations

List of all Bravais translations as defined for the centering of the current space group.

Mark all

Selects all symmetry matrices and all Bravais translations in the lists Symmetry operations and Bravais translations.

Unmark all

Resets the selections of all symmetry matrices and of all Bravais translations in the lists Symmetry operations and Bravais translations.

Select all

Selects all items in all lists, that means all atoms of the parameter list, all symmetry matrices, and all Bravais translations.

Remark

Decisive for the selection of atoms is the list Atoms from parameter list, whereas the list with the atom types does only support the selection of atoms. Usually you select first all atoms belonging to one or more atom types and then - if necessary - select or exclude special crystallographic different atoms.

Usually this function is used for the investigation of sublattices. To remind the user that a part of the structural data is suppressed, a warning symbol appears in the lower left corner of the structure window. (This triangle will not be printed.)

See also:

Filter: Overview


Filter off command (Build toolbar)

Resets the filter function for building up structures. Selects all atoms of the parameter list as well as all symmetry matrices and Bravais translations for building operations. The warning symbol in the lower left corner of the structure window will disappear.

See also:

Filter: Overview


Connectivity command
Connectivity command (Structure menu)

Opens the Connectivity dialog where you can select bonding spheres and their bonding ranges.

See also:

About Atoms, Atom Types, Bonds, and Bond Types: Connectivity


Connectivity dialog
Connectivity

Enables and disables bonds between selected pairs of atom types and their bonding spheres.

Select atom pair(s) to be connected

List of all N(N+1)/2 combinations of N atom types of the structure. The selected atom type pairs are marked. Given are both element symbols and (as far as defined) the oxidation numbers as well as the lower and upper bound of the bonding sphere (in Angstroem). This list uses the multiple selection feature, i.e. you may enable or disable atom type pairs independent from each other.

Evaluate

Resets all bonding spheres to the initial values (see below for Reset). Then calculates interatomic distances for each bonding sphere. An atom type pair (bond type) will then be selected, if at least one distance is found within the bonding sphere range.

Reset

Resets all bonding spheres to the initial values:

If a mean bond value is defined for the element combination of the atom type pair (bond type) (ignoring oxidation numbers) in the Diamond configuration file, this value is taken as mean value of the bonding sphere. Otherwise, the effective radii of the two atom types are added.

The result is multiplied with the lower sphere boundary factor to get the lower boundary value of the bonding sphere. The upper sphere boundary factor is used for the upper boundary value. Diamond works with default boundary factors of 0.6 and 1.2 rsp.

To edit the boundary factors, push the Settings button, and edit the values in the Settings for connectivity dialog.

All bond type are selected, unless the oxidation numbers have the same sign.

Connect

Connects all atoms on the basis of the presently (!) defined connectivity. This enables you to connect atoms belonging to specific atom types within a discrete bonding sphere without overwriting a previously built connectivity list. For details, see "Connecting All or Selected Atoms".

Settings

Opens the Settings for connectivity dialog, where you can edit both the lower and upper sphere boundary factor, as well as the mean bond values, which are used for the initialization or reset of the bonding spheres.

Bonding sphere

Displays a histogram of all distances between all atoms belonging to the selected atom type pair. The actual boundaries of the bonding sphere are given in DMin and DMax.

To change the dimensions of the bonding sphere, edit the lower and/or upper value in DMin and DMax rsp. or shift the red lines in the histogram.

To shift one of the red lines, move the mouse cursor to the line. (The mouse cursor changes its symbol.) Press the left mouse button and move the line to the desired position. When you have reached the final position, release the left mouse button. The new lower or upper value will be reflected in the DMin or DMax field as well as in the list Select atom pair(s) to be connected.

Please note that the calculation of the interatomic distances to be displayed in the histogram may take a while, especially for structures with some thousands of atoms in the parameter list (e.g. proteins).

See also:

About Atoms, Atom Types, Bonds, and Bond Types: Connectivity

Connecting All or Selected Atoms


Settings for connectivity dialog
Settings for connectivity

Defines lower and upper sphere boundary factor, the maximum distance in the histogram, and the list of mean bond lengths, which is used for the initialization or reset of bonding spheres. This dialog is called from the Connectivity dialog.

Lower sphere boundary factor

Defines the factor which is used to calculate the lower boundary of the bonding sphere.

Upper sphere boundary factor

Defines the factor which is used to calculate the upper boundary of the bonding sphere.

Upper distance limit for evaluation and histogram

Defines the maximum value that is used for the histogram in the Connectivity dialog.

Mean bond length values

List of all mean bond length values that are actually defined in the bond length section of the Diamond configuration file. For each entry, both element symbols and the mean bond length value in Angstroems are given.

Add

Adds the element combination and the distance value given in the three input fields below the list to the actual list of mean bond lengths.

Delete

Deletes the actually selected element combination from the list of mean bond lengths.

Replace

Overwrites the actually selected element combination and its mean bond length value with the values in the three input fields below the list.

See also:

About Atoms, Atom Types, Bonds, and Bond Types: Connectivity


Molecule cage command
Molecule cage command (Structure menu)

Opens the Molecule cage dialog to define

(1) 	the maximum depth of recursion,

(1) 	security borders for the molecular generator ("cage").

See also:

How the Molecular Generator Works

Special Settings for the Molecular Generator


Molecule cage dialog
Molecule cage

Defines the maximum depth of recursion as well as security borders for the molecular generator ("cage").

Maximum depth of recursion

Defines the maximum number of cycles when searching for bonded neighbours. If this number is reached during a molecular generation process, the structure may be polymeric. The maximum value is 128.

Crystal cage

Defines a parallel epiped with border values refering to the crystal coordinate system. The six border values are defined in the corresponding input fields XMIN, YMIN, ZMIN, XMAX, YMAX, and ZMAX. If the checkbox Active is checked, the molecular generator will stop for atoms outside these borders.

Cartesian cage

Defines a rectangular parallelepiped similar to the crystal box described above but with borders refering to the reference coordinate system (in Angstroems).

Spherical cage

Defines a sphere with center at XC, YC, ZC and the inner and outer bound RMIN and RMAX rsp.

Remark

Boxes and sphere may be activated independent from each other. The molecular generator will stop searching for neighbours, if an atom found lies outside at least one of these bodies. Atoms outside the boxes and/or sphere will be created but do not serve as starting point for a search for neighbours.

See also:

How the Molecular Generator Works

Special Settings for the Molecular Generator


Fill unit cell command
Fill | unit cell command (Structure menu)

Fills the contents of the unit cell of the current structure. Therefore the Epsilon value is considered, which is defined in the Diamond configuration file and can be changed in the Fill super cell dialog. This value avoids atoms on edges of faces of the unit cell from being excluded. With an Epsilon of e.g. 0.01, the range XMIN=YMIN=ZMIN= -0.01 and XMAX=YMAX=ZMAX= 1.01 of the lattice will be considered.

Cell edges will be generated automatically, if the setting Automatic generation of cell edges is switched on in the same dialog or in the current configuration.

See also:

Filling the Unit Cell


Fill super cell command
Fill | super cell command (Structure menu)

Opens the Fill super cell dialog, where you can fill the contents of a super cell consisting of multiple cells.

See also:

Filling a Super Cell


Fill super cell dialog
Fill super cell

This dialog is used to fill the contents of the unit cell or of a super cell, which consists of an integer multiple of the unit cell.

Select super cell

Defines the unit cell or the super cell, rsp., which has the following dimensions in crystal coordinates:

Type	XMIN	YMIN	ZMIN	XMAX	YMAX	ZMAX
Unit cell	0	0	0	1	1	1
Double cell X	-1	0	0	1	1	1
Double cell Y	0	-1	0	1	1	1
Double cell Z	0	0	-1	1	1	1
Quadruple cell XY	-1	-1	0	1	1	1
2 x 2 x 2 cells	-1	-1	-1	1	1	1
3 x 3 x 3 cells	-1	-1	-1	2	2	2
4 x 4 x 4 cells	-2	-2	-2	2	2	2

Epsilon value

Defines a value that will be subtracted from the lower bounds (XMIN, YMIN, ZMIN) of the unit cell or super cell and added to the upper bounds (XMAX, YMAX, ZMAX).

The epsilon value prevents atoms which are (nearly exactly) on edges or faces of the unit or super cell from being excluded during the filling procedure. If Epsilon is set to 0.01 e.g. the real cell range to be filled has XMIN=YMIN=ZMIN= -0,01 and XMAX=YMAX=ZMAX= 1,01 in crystal coordinates.

Create cell edges automatically

If this checkbox is checked, the cell edges of the unit cell will be created automatically when filling the contents of the unit cell. If a super cell is filled, all cell edges will be created automatically, too.

Apply

Fills the contents of the unit cell or super cell according to the current settings in this dialog box, but does not close the dialog.

Remarks

The settings for epsilon as well as the state of the checkbox Create cell edges automatically will be saved in the Diamond configuration file when closing the dialog and be available for later sessions of Diamond. Both settings affect the Fill unit cell command, too.

See also:

Filling the Unit Cell

Filling a Super Cell


Fill cell range command
Fill | cell range command (Structure menu)

Opens the dialog box Fill cell range, where you can define a parallelepiped in crystal, reference or view coordinates, to be filled with atoms.

See also:

Filling a Cell Range


Fill cell range dialog
Fill cell range

Fills the contents of a parallelepiped, which can be defined using crystal, reference, or view coordinates.

Limits

Defines the border values of the parallelepiped XMIN, YMIN, ZMIN, XMAX, YMAX, and ZMAX.

Coordinate type

Defines the type of coordinate system, which the six values in Limits refer to:

Crystal coordinates	The border values refer to the axes a, b, c of the unit cell. The values given (x/a, y/b, z/c) have no dimensions.
Reference coordinates	The border values refer to the axes of the reference coordinate system and describe a parallelepiped which is rectangular in any case, with values of dimension Angstroem.
View coordinates	The border values refer to the axes of the view coordinate system and describe a rectangular parallelepiped with dimension Angstroem, too.
Create cell edges automatically

If this checkbox is checked, cell edges will be created automatically when filling the contents of the given cell range.

See also:

Filling a Cell Range


Fill box command
Fill | box command (Structure menu)

Opens the dialog Fill box, where you can fill the contents of a parallelepiped with defined radii and an atom of the parameter list as center.

See also:

Filling Boxes or Spheres Around Selected Atoms


Fill box dialog
Fill box

Fills the contents of a parallelepiped with defined radii and an atom of the parameter list as center.

Select center from parameter list

List of the atoms of the parameter list. Element symbol, symbol, oxidation number, Wyckoff symbol, x, y, z and site occupation (as far as defined and less than 1) are given.

Atom code

The code of the atom which will be taken as central atom of the box, if this dialog is closed with OK. By default, this code corresponds to the atom which is actually selected in the parameter list, and does not contain any symmetry operations, Bravais translations and integer cell translations. These additional operations can be selected in the Choose central atom dialog, which is called via the Select center button.

Select center

Opens the Select central atom dialog, where you select a symmetry operation, Bravais translation as well as the integer cell translations for the code in Atom code.

Radii

Defines the radii of the parallelepiped in the input fields DX, DY and DZ with dimensions depending on the coordinate system chosen:

Crystal coordinates	The radii refer to the axes a, b, c of the unit cell. The values given (x/a, y/b, z/c) have no dimensions.
Reference coordinates	The radii refer to the axes of the reference coordinate system and describe a parallelepiped which is rectangular in any case, with values of dimension Angstroem.
View coordinates	The radii refer to the axes of the view coordinate system and describe a rectangular parallelepiped with dimension Angstroem, too.

See also:

Filling Boxes or Spheres Around Selected Atoms


Fill sphere command
Fill | sphere command (Structure menu)

Opens the Fill sphere dialog, where you can fill the contents of a sphere with specific inner and outer bound and a selected atom from the parameter list as center.

See also:

Filling Boxes or Spheres Around Selected Atoms


Fill sphere dialog
Fill sphere

Fills the contents of a sphere with specific inner and outer bound and a selected atom from the parameter list as center.

Select center from parameter list

List of the atoms of the parameter list. Element symbol, symbol, oxidation number, Wyckoff symbol, x, y, z and site occupation (as far as defined and less than 1) are given.

Atom code

The code of the atom which will be taken as central atom of the sphere, if this dialog is closed with OK. By default, this code corresponds to the atom which is actually selected in the parameter list, and does not contain any symmetry operations, Bravais translations and integer cell translations. These additional operations can be selected in the Choose central atom dialog, which is called via the Select center button.

Select center

Opens the Select central atom dialog, where you select a symmetry operation, Bravais translation as well as the integer cell translations for the code in Atom code.

Radii

Defines the inner and outer bound of the sphere in the input fields RMinand RMax in Angstroems.

See also:

Filling Boxes or Spheres Around Selected Atoms


Choose central atom dialog
Choose central atom

Defines sequential number of the atom in the parameter list, which is used as center of a parallelepiped or sphere, as well as the symmetry operation, Bravais translation and integer cell translations.

Atom from parameter list

List of all atoms of the parameter list. The atom coded in Atom code, is currently selected.

Symmetry operation

List of all symmetry operations (symmetry matrices) of the current space group. The symmetry operation coded in Atom code is currently selected.

Bravais translation

List of all Bravais translations of the current space group. The Bravais translation coded in Atom code is currently selected.

Cell translations

The three integer cell translations in the a-, b-, and c-direction of the unit cell axes, as coded in the current Atom code.

Atom code

The current atom code according to the current selections in the lists and input fields X, Y, and Z.

See also:

Filling Boxes or Spheres Around Selected Atoms


Fill area command
Fill | area command (Structure menu)

Fills the contents of a rectangular box of the lattice with borders referring to the view coordinate system. X- and y-dimension are defined by a user-defined rectangle, the z-dimension by manual input of two border values ZMIN and ZMAX.

See also:

Filling a Rectangular Area of the Screen


Add all atoms command
Add all atoms command (Structure menu)

Creates atoms from all atoms defined in the parameter list without applying symmetry operations or cell translations. This command is suitable, if the parameter list describes one or more complete molecules.

See also:

Adding All Atoms of Parameter List


Add atoms command
Add atoms command (Structure menu)

Opens the Add atoms dialog, where you can generates atoms from the parameter list by defining atom codes or atom code ranges or by selecting atoms and symmetry operations from lists.

See also:

Adding Some Atoms from Parameter List


Add atoms dialog
Add atoms

Generates atoms from the parameter list by defining atom codes or atom code ranges or by selecting atoms and symmetry operations from lists.

Atoms from parameter list

List of all atoms of the parameter list. Element symbol, symbol, oxidation number, Wyckoff symbol, x, y, z and site occupation (as far as defined and less than 1) are given. This list has extended selection, i.e. single or multiple atoms may be selected.

Symmetry operations

List of all symmetry matrices of the current space group (extended selection possible).

Bravais translations

List of all Bravais translations of the current space group (extended selection possible).

Integer cell translations

Defines if or what (integer) cell translations are to be applied along the three axes of the crystal coordinate system. E.g. define the lower and upper bound for integer cell translations along the a-axis of the lattice in the input fields to the left and right of <= X <=. 0 means that no cell translations are to be applied (for that direction).

Reset selections

Clears all selections in the lists of atomic parameters, symmetry operations, and Bravais translations. Then the identity symmetry operation "x,y,z" and Bravais translation "+(0,0,0)" will be selected. Neither integer cell translations nor the contents of the Code(s) input field will be affected.

Code(s)

Input field for the definition of one or more atom codes or atom code ranges. See the article "Adding Some Atoms from Parameter List" how to define atom codes or atom code ranges.

Apply

Starts the generation of all selected atoms. All atoms selected in the parameter list will be applied to all selected symmetry operations, Bravais translations and integer cell translations. Additionally the atom codes in Code(s) will be evaluated, and atoms generated. This is the same what OK would do, but without closing the dialog.

See also:

Adding Some Atoms from Parameter List


Insert atom command
Insert atom command (Structure menu)

Inserts a new atom in the center of two or more selected atoms. This atom will be appended as dummy atom to the parameter list.

See also:

How to Insert an Atom


Insert atom dialog
Insert atom

This dialog is called by the Insert atom command in the Structure menu to define or confirm the symbol as well as the crystal coordinates for a dummy atom that may be appended to the atomic parameter list.

Atom symbol

Defines the atom symbol for the new atom in the parameter list, which is "Dummy" by default or "Dummy2", etc. for the second, third, etc. dummy atom. You may change the atom symbol afterwards by choosing the Atomic parameters command from the Edit menu.

X, Y, Z

These input fields define the position of the dummy atom in crystal coordinates. This position is the center of the atoms that have been selected before the Insert atom command has been called. You may change these values, if you want to override the calculated center of the selected atoms.

Create atom at current position

If this checkbox is checked, an atom will be generated at the new position. Otherwise only the "asymmetric" atom will be added to the atomic parameter list. A new dummy atom is added to the parameter list only if there is not yet a dummy atom on the "asymmetric" position. If there is already a dummy atom on the "asymmetric" position and this checkbox is checked, Diamond creates a symmetry equivalent atom from this position.

See also:

How to Insert an Atom


Spheres command (Structure menu)

Opens the Define fixed sphere dialog to define the border values of an enclosure sphere. Fills spheres around selected atoms or around all atoms, if no atom has been selected.

If this command has been called from the Build toolbar using the [image] button, the Define fixed sphere dialog is not displayed, and the border values of a previous call of the Define fixed spheres dialog are used.

See also:

Fixed vs. Coordination Spheres

Filling Fixed Spheres


Define fixed sphere dialog
Define fixed sphere

This dialog is used by the Spheres command in the Structure menu to define the lower and upper boundary of an enclosure sphere. This fixed sphere will be applied to all atoms, if no atom has been selected, of to the selected atoms only.

RMin

Defines the lower boundary of the fixed sphere in Angstroems.

RMax

Defines the upper boundary of the fixed sphere in Angstroems.

See also:

Fixed vs. Coordination Spheres

Filling Fixed Spheres


Coordination spheres command (Structure menu)

Opens the Fill coordination spheres command, where you can define coordination spheres by atom types, and generate the corresponding atoms.

If this command has been called from the context menu of one or more selected atoms, from the Build toolbar using the [image] button or from the accelerator key Shift+Ctrl+S, coordination spheres are filled around selected atoms or around all atoms, if no atom has been selected. Ligand atoms are created only, if defined by connectivity.

See also:

Fixed vs. Coordination Spheres

Filling Coordination Spheres Around Selected Atom Types


Fill coordination spheres dialog
Fill coordination spheres

Generates atoms belonging to selected atom types within coordination spheres around atoms belonging to selected atom types.

Central atoms

List with all atom types of the current compound, that may be selected as central atoms of spheres. Only atoms of the marked types will be taken into consideration as centers. This list works with multiple selectionref_listextendedsel, i.e. you can select items independent from each other.

Ligand atoms

List with all atom types of the current compound, that may be selected as ligand atoms of coordination spheres. Only atoms of the marked types will be taken into consideration as ligand atoms. Like Central atoms, this list works with extended selection.

Number of cycles

Defines how often the procedure of filling coordination spheres is to be carried out.

Create broken-off bonds

If this checkbox is checked, ligand atoms will be declared as invisible and bonds to these ligand atoms will be drawn shorter than common bonds ("broken-off bonds"). These bonds pointing into space are often used to illustrate infinite structures.

Apply

Starts generating atoms within the coordination spheres around all atoms belonging to the types selected in Central atoms considering only atoms of the types selected in Ligand atoms as ligand atoms. Unlike OK, this will not close the dialog.

See also:

Fixed vs. Coordination Spheres

Filling Coordination Spheres Around Selected Atom Types

Filling Coordination Spheres in Multiple Cycles

Creating Broken-off Bonds


Molecules command (Structure menu)

Creates molecules from the atoms of the parameter list.

The filter function, the definition of connectivity, as well as the "molecule cage" may take affect on the generation of molecules.

See also:

Molecules: Overview

Generating Molecules from Parameter List


Complete fragments command (Structure menu)

Completes all fragments to molecules, if no atom is selected. If atoms are selected, only molecules are completed, which the selected atoms belong to.

The filter function, the definition of connectivity, as well as the "molecule cage" may take affect on the generation of molecules.

See also:

Molecules: Overview

Completing Molecular Fragments

Packing Diagrams


Connect atoms command (Structure menu)

Generates bonds between all selected atoms, as far as defined by the current connectivity list. If no atoms is selected, all atoms are connected as far as defined in the connectivity list.

See also:

Connecting All or Selected Atoms

Connectivity


Insert bonds command
Insert bonds command (Structure menu)

Switches to a mode where you can generate a bond between two selected atoms each. The bond will be created even if no bonds have been defined in the connectivity list for this atom type combination, and even if the bond is "too short" or "too long" (that means not within the bonding sphere). While you are in Insert Bonds mode, the mouse cursor changes to a special symbol. You can end this mode by calling this command again or simply by pressing the Esc key.

See also:

Inserting a Bond Between Two Atoms


Insert bond command
Insert bond command (Build toolbar)

Generates a bond between two selected atoms. The bond will be created even if no bonds have been defined in the connectivity list for this atom type combination, and even if the bond is "too short" or "too long" (that means not within the bonding sphere).

See also:

Inserting a Bond Between Two Atoms


Destroy molecule(s) command (Structure menu)
Destroy | molecule(s) command (Structure menu)

Deletes the molecule(s) where the selected atom(s) belong to.

See also:

Deleting Molecules or Fragments


Destroy fragment(s) command (Structure menu)
Destroy | fragment command (Structure menu)

Deletes the fragment which is defined by the two selected atoms. This function deletes the bond between the selected atoms, and then deletes the molecular rest where the second atom belongs to.

See also:

Deleting Molecules or Fragments


Destroy polyhedra command (Structure menu)
Destroy | polyhedra command (Structure menu)

Deletes all selected coordination polyhedra. A coordination polyhedron is selected, if its central atom is selected. Atoms belonging to a polyhedron coordination sphere will not be destroyed, but only the polyhedron faces between.

See also:

Destroying Polyhedra


Destroy non-bonded atoms command (Structure menu)
Destroy | non-bonded atoms command (Structure menu)

Deletes all atoms which are not involved in bonds.

See also:

Deleting Atoms or Bonds


Destroy all command (Structure menu)
Destroy | all command (Structure menu)

Deletes the entire structural part, that means all created atoms and thus all bonds between them, cell edges and coordination polyhedra. Text(s) in the structure window (but not labels) will remain.

See also:

Destroying the Structure Picture


Destroy atom(s) command (context menu)
Destroy | atom(s) command (context menu)

Deletes all selected atoms. Other selected objects like bonds, labels etc. are not affected.

See also:

Deleting Atoms or Bonds


Destroy bond(s) command (context menu)
Destroy | bond(s) command (context menu)

Deletes all selected bonds. Other selected objects like atoms, labels etc. are not affected.

See also:

Deleting Atoms or Bonds


Destroy atom label(s) command (context menu)
Destroy | atom label(s) command (context menu)

Deletes all selected atom labels. Other selected objects like bond labels, atoms, bonds, texts, will not be affected.

See also:

Removing Labels


Destroy bond label(s) command (context menu)
Destroy | bond label(s) command (context menu)

Deletes all selected bond labels. Other selected objects like atom labels, atoms, bonds, texts, will not be affected.

See also:

Removing Labels


Cell edges command (Objects menu)

Opens the Cell edges dialog, where you can add, edit, or delete cell edges.

See also:

Cell Edges: Overview


Add unit cell edges command (toolbar/hotkey)
Add unit cell edges command

Creates the edges of the unit cell without opening the Cell edges dialog. The design of the cell edges will be the default cell edges design or the cell edges design which has been set the last time the Cell edges dialog was open.

See also:

Adding Cell Edges


Cell edges dialog
Cell edges

Adds specific cell edges to the structure picture, deletes all cell edges, or defines color and line style of the cell edges.

Range

The input fields XMIN to ZMAX limit the range of the cell edges. The range XMIN=YMIN=ZMIN=0 and XMAX=YMAX=ZMAX=1 defines e.g. the unit cell. Only integer numbers are valid in the input fields.

Style

Defines color, style, and thickness of the cell edges. The color can be selected from the combobox Color. The line style is defined in Style. The thickness of solid lines in millimeters can be set in Thickness. Dashed or dotted lines have a width of one pixel in any case.

Build

Generates cell edges according to the border values defined in the input fields XMIN to ZMAX. The current color and style are assigned to the new cell edges. Previously defined cell edges within the mentioned range will be updated.

Delete all

Deletes all previously generated cell edges.

Update styles

Updates colors, styles, and thicknesses of all previously generated cell edges.

Enhance cell edge drawing

This setting affects only drawings in standard mode. In standard mode, Diamond sorts all objects for increasing z-coordinates (view coordinate system). After an atom has been drawn, all bonds connected with that atom and which do not point backwards will be drawn immediately after.

If this checkbox is not checked, cell edges are treated like bonds when drawing. (The cell corners are used as invisible pseudo-atoms.) Since cell edges may be very long and thus interpenetrate larger parts of the structure picture, this may lead to wrong overlap between real atoms and bonds and cell edges.

If this checkbox is checked, Diamond draws each cell edge in several steps to avoid overlap with atoms and bonds that may cut the projection of the cell edge.

See also:

Cell Edges: Overview


Thermal ellipsoids command (Objects menu)

Opens the Thermal ellipsoids dialog to define if and how thermal ellipsoids are to be displayed.

See also:

Thermal Ellipsoids: Overview


Thermal ellipsoids dialog
Thermal ellipsoids

Defines if and how thermal ellipsoids are to be displayed.

Display thermal ellipsoids

If this checkbox is checked, atoms are represented as thermal ellipsoids, else as circles.

Draw basic ellipses only

If this checkbox is checked, Diamond suppresses all atom styles and draws only the three basic ellipses of each ellipsoid. The ellipsoid is not filled, i.e. it is transparent. This setting has the advantage that open ellipsoids are drawn almost as quick as normal circles, but you can still estimate the dimensions of the ellipsoid - e.g. when positioning atom labels.

Draw lines on back sides, too (Octands)

If this checkbox is checked, the program draws even the back parts of the basic ellipses if an ellipsoid is shaped with an open octand.

Solid lines on back side

If this checkbox is checked, the back parts of the basic ellipses are drawn as solid instead of interrupted lines.

Hatching (octands)

Defines how to hatch the three walls of an open octand. You may either determine the number of hatching lines for each wall (Number) or determine a fixed distance between these lines (in Angstroems, Distance). Valid values are 0 to 31 lines per wall and 0.001 to 0.25 Angstroem, rsp.

Probability factor (Percent)

Defines indirectly the size of the ellipsoids. The default value is 50 percent.

See also:

Thermal Ellipsoids: Styles

Displacement Parameters and Ellipsoid Representation


Atom labels command (Edit menu)
Atom labels command (Objects menu)

Opens the Add atom labels dialog to define contents, position, size, font, and color of atom labels to be added to the selected atoms. If at least one existing atom label is selected, but no atoms are selected, the Edit atom labels dialog is opened instead, which is almost identical with the Add atom labels dialog.

See also:

Labelling Atoms And Bonds: Overview


Add/Edit atom/bond labels dialog
Add/Edit atom/bond labels

This dialog is used to define the contents, position, size, font, and color of atom labels as well as bond labels. It is used both to edit existing labels as well as to define new labels.

Text

Defines the contents of the atom label or bond label. The label can either have individual text or pre-defined text such as the atom symbol or the bond length. Content determines the kind of information to be supplied, whereas Format decides how the information will be formatted.

For atom labels, you may select from:

Content	Format	Description
Element symbol	Fe	Formats the element symbol: First letter uppercase, second (if defined) lowercase.
	FE	Both letters (as far as defined) uppercase.
Atom symbol	Fe 1	Formats the atom symbol without any change.
	Fe1	Formats the atom symbol, but removes blanks, e.g. blanks between an element symbol and additional identifiers.
	Fe^1^	Formats the atom symbol with the non-element part of the symbol as far as possible as superscript.
	Fe~1~	dito, but as subscript.
Atom identifier	AXYZSSB	Formats the atom code.
	PARM #	Formats the sequential number of the atom in the parameter list (beginning with #1).
	ATOM #	Formats the sequential number of the atom in the list of created atoms (beginning with #1).
Element/Charge	Fe+2	Displays the element symbol plus charge or (formal) oxidation number. Charge is added to the element symbol directly as integer with sign (even if positive).
	Fe(+2)	The integer charge following the element symbol is enclosed in parentheses.
	Fe+2.345	Charge is added to the element symbol without rounding.
	Fe(+2.345)	The charge is enclosed in parentheses and not rounded.
	Fe^+2^	Like Fe+2, but with charge as superscript.
	Fe^+2.345^	Like Fe+2.345, but with charge as superscript.
	Fe^2+^	Charge is rounded and superscripted with sign following the charge.
Charge	+2	Displays the charge (or formal oxidation number), as far as defined. Charge is rounded and signed even if positive.
	2	Charge is rounded and signed if negative.
	+2.345	Charge is signed even if positive but not rounded.
	2.345	Charge is signed if negative and not rounded.
(Individual text)		The label contains individual text which has to be entered or changed in the input field Individual text.

For bond labels, you may select from:

Content	Format	Description
Bond length	1.234	Formats the bond length in Angstroems without unit symbol.
	123.4	Formats the bond length in picometers without pm symbol.
	1.234 Å	Formats the bond length in Angstroems with unit symbol.
	123.4 pm	Formats the bond length in picometers with pm symbol.
	1.234(5)	Like 1.234 but with standard uncertainty, as far as defined.
	123.4(5)	Like 123.4 but with standard uncertainty, as far as defined.
	1.234(5) Å	Like 1.234 Å but with standard uncertainty, as far as defined.
	123.4(5) pm	Like 123.4 pm but with standard uncertainty, as far as defined.
Identifier	BOND #	The sequential number of the bond in the list of created bonds (beginning with #1).
(Individual)		The label contains individual text which has to be entered or changed in the input field Individual text.

Style

This group defines the position, size, color, font, and additional styles for the label.

Relative position (X, Y, Z)

X and Y define the distance between the reference point of the label and the center of the corresponding atom in Angstroems. The first value determines the horizontal, the second one the vertical distance. Positive values mean shift to the right and top rsp. The reference point of the label is defined by Alignment.

Z is used only for rendered structure pictures to define the 3D position of the text relative to the 3D coordinates of the corresponding atom. See the article "Labelling Atoms And Bonds: Style, Size, and Position" for details.

Alignment

Defines the reference point within the rectangle that surrounds the label text. This takes effect on the Relative position (X, Y, Z).

Centered	the horizontal and vertical center of the label
Right	the left edge and the vertical center (text appears right from the reference point)
Left	the right edge and the vertical center (text appears left from the reference point)
Parallel	the label text is rotated with the bond axis (bond labels only)

Text size

Defines the size of the atom label in Angstroem.

Color

Defines the color of the label text.

Use atom's (bond's) main color

If this checkbox is checked, the Color checkbox is not available, and the main color of the atom or bond, rsp., will be assigned to the label. The main color is derived from the atom's or bond's design: The main color is the interior color of atoms and thick bonds. (For thin bonds, only one color is available.) If the atom or thick bond is hollow or has black or white as interior color, Diamond takes the edge color instead.

Font

Calls the MS Windows standard dialog Font to define the font and attributes like bold and/or italics.

Underline

If this checkbox is checked, the label text will be underlined.

Strike out

If this checkbox is checked, the label text will be struck out.

Opaque

If this checkbox is checked, the label text will be opaque, which means that the background of the label text will be filled with the current background color. Otherwise (default) it is transparent.

Update existing label definitions [Add atom/bond labels dialog only]

This setting applies to atoms or bonds, rsp., which still have a label. If this checkbox is checked, existing label settings will be overwritten with the current contents, color, font, position, and size. Otherwise existing labels will be left unchanged.

Use this design as default for new labels [Edit atom/bond labels dialog only]

If this checkbox is checked, the current settings for contents, position, size, font, and color will be stored in the Diamond configuration as default setting for new atom labels or bond labels.

Apply

Applies the current settings to the selected labels, if labels are to be edited, or adds labels to the selected atoms or bonds, rsp., without closing the dialog. (OK will do the same but close the dialog.)

Remarks

Since both position and size of the label are given in Angstroems rather than in centimeters or millimeters, both position and size of the label depend on the current enlargement factor of the structure picture. If central projection is used, labels in the front may appear larger than those in the rear.

Normally, labels do not rotate when the structure is being rotated. Especially for bond labels, you can assign an alignment that rotates bond labels automatically so that the text is parallel with the bond axis. (See Alignment.)

Each label is assigned to a specific atom or bond, rsp. This makes it impossible to label one atom or bond, rsp., twice or more times.

The position of labels can be shifted with the mouse afterwards. See the article "Shifting Position With Mouse or Cursor" how this can be done.

See also:

Labelling Atoms and Bonds: Overview


Bond labels command (Objects menu)

Opens the Add bond labels dialog to define contents, position, size, font, and color of bond labels to be added to the selected bonds. If at least one existing bond label is selected, but no bonds are selected, the Edit bond labels dialog is opened instead, which is almost identical with the Add bond labels dialog.

See also:

Labelling Atoms And Bonds: Overview


Add label(s) command (Build toolbar)

Adds label(s) to the selected atom(s) and/or bond(s). Font, size, position and color of the labels will have the settings from the latest call to the Add atom labels dialog or Add bond labels dialog, rsp., or the default settings.

See also:

Labelling Atoms and Bonds: Overview


Text command (Objects menu)

Opens the Add text dialog, where you can define contents, position, size, font, and color of an individual text at an arbitrary position within the structure picture. If existing text is selected, the Edit text dialog is opened instead, which is almos identical with the Add text dialog.

See also:

Text: Overview


Add/Edit text dialog
Add/Edit text

This dialog is used to define the contents, position, size, font, and color of text that can be placed at an arbitrary position within the structure picture. It is used both to edit existing text as well as to add a new text to the structure picture.

Text

Defines the contents of the text string. This text can be either defined individually or as text field. The text string or the text field definition, rsp., itself is defined in the input field Text. The Get pushbutton gives you access to pre-defined text strings, which can be copied directly as text or indirectly as text field to the input field Text.

A text field has the form "{FIELD=<FIELDNAME>}", e.g. "{FIELD=FORMULA_SUM}" for the formula sum. The following field names are available:

<FIELDNAME>	Description
TITLE	the title of the publication or of the compound,
AUTHORS	the name(s) of the author(s),
NAME_COMMON	the common (usual, trivial) name of the compound,
NAME_SYSTEMATIC	the systematic (IUPAC) name of the compound,
NAME_MINERAL	the mineral name of the compound,
NAME_STRUCTURETYPE	the name of the structure type,
FORMULA_SUM	the formula sum, which has been generated from the atomic parameter list,
FORMULA_STRUCTURAL	the structural formula, which is defined as bibliographic data,
FORMULA_ANALYTICAL	the analytical formula, which is defined as bibliographic data,
FORMULA_TYPE	the formula type, which has been generated from the atomic parameter list,
PEARSONCODE	the Pearson symbol, which has been generated from the atomic parameter list and the current space group,
WYCKOFFSEQUENCE	the Wyckoff sequence, which has been generated from the atomic parameter list.

Text fields have the advantage that they will be updated automatically when the structural data have been changed, whereas invidual text is not updated.

Individual text and text fields may be mixed together, e.g. "Formula: {FIELD=FORMULA_STRUCTURAL}"

Style

Defines font, color, position, size, and additional styles for the text.

Position relative to center of picture

Defines the horizontal (left input field) and vertical (right input field) distance of the reference point of the text string from the center of the picture (or from the center of the structure window, rsp.), in centimeters. Positive values mean shift to the right and top rsp. The reference point of the text string consists of the left edge of the first character and the baseline of the text.

Text size

Defines the height of a character cell of the text in centimeters. This is the vertical distance between bottom and top line of the font.

Color

Defines the color of the text string.

Font

Calls the MS Windows standard dialog Font to define the font and attributes like bold and/or italics.

Underline

If this checkbox is checked, the label text will be underlined.

Strike out

If this checkbox is checked, the label text will be struck out.

Use this style as default for new labels [Edit text dialog only]

If this checkbox is checked, the current settings for position, size, font, and color will be stored in the Diamond configuration as default setting for new text.

Apply [Edit text dialog only]

Applies the current settings to the selected texts, if text is to be edited, or adds text to the structure picture, rsp., without closing the dialog. (OK will do the same but close the dialog.)

Remarks

In any case, the position of a text refers to the center of the structure window (or structure picture rsp.). That means text does not move if the structure is shifted or rotated. The size of the text does not vary with the enlargement factor.

Control characters (e.g. for super- or subscript) may be used within text strings. See the article "About control characters in text strings" for details. A text string must not include carriage return or line feed. For multiline text you have to define multiple text strings with different vertical positions but the same horizontal position.

Text may be shifted afterwards with the mouse. See the article "Shifting Position With Mouse or Cursor" how this can be done.

See also:

Text: Overview


Get text dialog
Get text

Used to select a pre-defined text string to be inserted in the text input field of the Edit text dialog or Add text dialog.

The list contains several bibliographic data as well as text strings, that have been formatted by Diamond, e.g. the formula sum, which has been generated from the atomic parameter list.

Insert selected text as field

If this checkbox is checked, the selected text will be inserted as text field, otherwise directly. For details see "Using Text Fields".

See also:

Text: Overview


Coordinate system command (Objects menu)

Opens the Coordinate system dialog, which defines if, where and how to display the coordinate system in the structure window/picture. This coordinate system represents the current orientation.

See also:

Coordinate System: Overview


Coordinate system dialog
Coordinate system

Defines if, where and how to display the coordinate system in the structure window/picture. This coordinate system represents the current orientation.

Display coordinate system

Only if this checkbox is checked, the coordinate system will be displayed.

Labels

Determines what kind of coordinate system the three axes to be displayed shall refer to:

a, b, c	The axes represent the axes of the crystal coordinate system, i.e. the cell vectors a, b and c.
x, y, z	The axes represent the axes of the reference coordinate system.

Arrowheads

If this checkbox is checked, arrowheads are assigned to the tops of the axes of the coordinate system.

Position

Define the horizontal and vertical position of the origin of the coordinate system relative to the reference point (center of structure picture or one of the four corners rsp. - see Relative to). These values are given in centimeters. Positive values grow to the right and top rsp., negative values to the left and bottom rsp.

Relative to

Defines whether the coordinate system's position refers to the center of the structure picture of to one of the four corners:

center of picture	the values in X and Y define the horizontal and vertical distance of the origin of the displayed coordinate system from the center of the structure picture or the center of the structure window, rsp., in centimeters.
top left	the values in X and Y define the horizontal and vertical distance of the origin of the displayed coordinate system from the upper left corner of the structure picture or the structure window, in centimeters. This means, the position of the coordinate system depends on the size of the structure window (or of the page, if page view mode is used or when printed).
top right	dito, but referring to the upper right corner instead.
bottom left	dito, but referring to the lower left corner instead.
bottom right	dito, but referring to the lower right corner instead.

Axes' lengths

Defines the maximum length of an axis of the coordinate system given in centimeters, that means the size of the coordinate system. An axis has maximum length if it is arranged parallel to the drawing area, else it is shorter corresponding to its projection.

Axes' thickness

Defines the thickness of the lines which represent the axes, in millimeters.

Font size

Defines the size of the font, in centimeters.

Font

Opens the MS Windows standard dialog Font to select a font for the axis labels. The attributes bold and italics will be ignored.

Color

Defines the color used for the axes and labels.

Apply

Applies the current settings to the coordinate system without closing the dialog.

Remarks

The coordinate system's position refers to either the center of the structure picture (or the structure window rsp.) or to one of its four corners. If you want to align the coordinate system to special objects of the structure picture, you should set Relative to to center of picture. In this case the position remains even if you change the window's size or if you print the structure picture. When using relative positioning, the coordinate system's position adjusts automatically to its window's size. That leads to different absolute positions of the coordinate system on screen and printout rsp. See also "Coordinate System: Relative vs. Absolute Positioning".

The coordinate system does only represent the current orientation but does not symbolize the basis vectors a,b,c of the cell. See "Displaying the Unit Cell Axes" how the cell axes' representation may be switched on or off.

See also:

Coordinate System: Overview


Legend command (Objects menu)

Opens the Legend dialog, which defines if, where and how a legend of the atom types of the currently active structure is to be displayed in the structure window/picture.

See also:

Legend of Atom Types: Overview


Legend dialog
Legend

Defines if, where and how a legend of the atom types of the currently active structure is to be displayed in the structure window/picture.

Display legend

Only if this checkbox is checked, the legend will be displayed.

Position

Define the horizontal and vertical position of the reference point of the legend relative to the center of the structure picture or one of the four corners rsp. - see Relative to). These values are given in centimeters. Positive values grow to the right and top rsp., negative values to the left and bottom rsp.

Relative to

Defines whether the legend's position refers to the center of the structure picture of to one of the four corners:

center of picture	the values in X and Y define the horizontal and vertical distance of the centerpoint of the legend from the center of the structure picture or the center of the structure window, rsp., in centimeters.
top left	the values in X and Y define the horizontal and vertical distance of the upper left corner of the legend from the upper left corner of the structure picture or the structure window, in centimeters. This means, the position of the legend depends on the size of the structure window (or of the page, if page view mode is used or when printed).
top right	the values in X and Y define the horizontal and vertical distance of the upper right corner of the legend from the upper right corner of the structure picture or the structure window, in centimeters.
bottom left	the values in X and Y define the horizontal and vertical distance of the lower left corner of the legend from the lower left corner of the structure picture or the structure window, in centimeters.
bottom right	the values in X and Y define the horizontal and vertical distance of the lower right corner of the legend from the lower right corner of the structure picture or the structure window, in centimeters.

Atomic radii

Defines whether the radii of the atom types in the legend shall represent the atomic or ionic radii actually used for drawing - or not:

fixed	All atoms in the legend have the same size (the radius is given in Radius in centimeters).
atom-type-specific	The radii are used which have actually been used for drawing, that means the legend's size depends on the current enlargement factor.

Radius

Defines the radius which is used for every atom which is displayed in the legend, in centimeters. This field is used only when Atomic radii is set to fixed.

Font size

Defines the size of the font in centimeters.

Font

Opens the MS Windows standard dialog Font to select a font for the axis labels. The attributes bold and italics will be ignored.

Border width

Defines the thickness of the line which is used for the border of the legend, in millimeters. If this value is zero, no border will be drawn.

Color

Defines the color used for both frame and text of the legend.

Symbols

Defines if and how atom type symbols shall be formatted:

(no re-formatting)	The atom type symbol is not re-formatted.
superscript extension	If the atom type symbol consists of an element symbol and an attached extension (e.g. the oxidation number), the extension will be superscripted.
subscript extension	dito, but subscripted.

Select

Opens the Select Atom Types For Legend dialog where you can select which atom types may be mentioned in the legend.

Remarks

The legend's position refers to either the center of the structure picture (or the structure window rsp.) or to one of its four corners. If you want to align the legend to special objects of the structure picture, you should set Relative to to center of picture. In this case the position remains even if you change the window's size or if you print the structure picture. When using relative positioning, the legend's position adjusts automatically to its window's size. That leads to different absolute positions of the legend on screen and printout rsp. See also "Legend: Relative vs. Absolute Positioning".

See also:

Legend: Overview

Atom Types


Select Atom Types for Legend dialog
Select atom types for legend

Enables or disables the display of each atom type of the current structure in the legend of atom types.

Atom types

List of all atom types of the current structure. By default, all atom types are checked, that means will be displayed. By unchecking the corresponding checkbox in the list, you can hide the display of the atom type in the legend.

Hide atom types not used in structure picture

If this checkbox is checked, only those atom types with at least one corresponding created atom in the structure picture will be listed in the legend. Otherwise, all atom types of the atom type list will be listed.

See also:

Legend: Overview

Atom Types


Polyhedra command (Objects menu)

If one or more atoms are selected, which are all central atoms of coordination polyhedra, the Edit polyhedra dialog is opened, where you can change the design of the selected polyhedron or polyhedra, rsp.

If no atoms are selected or if one or more atoms are selected, which are not (yet) central atoms of coordination polyhedra, the Add polyhedra dialog is opened, which will create coordination polyhedra. The polyhedra will be created with the selected atom(s) as central atom(s) or with all created atoms as central atoms that belong to selected atom types.

See also:

Coordination Polyhedra: Overview


Add polyhedra command (context menu)

Opens the Add polyhedra dialog to create coordination polyhedra with the selected atoms as central atoms.

If this command has been called from the Build toolbar or with the accelerator Shift+Ctrl+H, the Add polyhedra dialog will not be displayed, and the polyhedra will be created automatically with the default or previous settings from the Design for new polyhedra dialog.

See also:

Coordination Polyhedra: Overview


Edit polyhedra command (context menu)

Opens the Edit polyhedra dialog where you can change the design of existing polyhedra.

See also:

Coordination Polyhedra: Overview


Add polyhedra dialog
Add polyhedra

Creates coordination polyhedra around all created atoms that belong to selected atom types (if no atoms have been selected) or around all selected atoms.

Central atoms

List of all atom types of the current compound. This list does not appear, if at least one atom has been selected. The selected atom types will be taken as centers for coordination polyhedra. This list works with multiple selection, that means multiple atom types may be selected independent from each other.

Ligand atoms

List of all atom types of the current compound. The selected atom types will be taken as ligand atoms of coordination polyhedra.

Type of sphere

Defines if the coordination spheres of the polyhedra depend on the atom types of central atom and ligand atoms or have a fixed size:

Generic	The size of the sphere (inner and outer bound) depends on the types of central and ligand atom and is defined in the connectivity.
Fixed	Inner and outer bound of the sphere are defined by RMin and RMax in Angstroems.

Angle epsilon

Defines an angle used for the extension of triangular polyhedron faces to polygons with four or more edges.

For each polyhedron, Diamond tries to extend the initially built triangular faces to polygons with four or more edges. For that, additional points are checked whether they are positioned approximately in the plane formed by the points of the triangle. If such a point encloses an angle of less than Angle epsilon degrees with the plane, it will be added to the triangle leading to a square, pentagon, etc. For details, see the article "Getting Polygons Greater Than Triangles".

Overwrite existing polyhedra

If this checkbox is checked, existing polyhedra will be deleted and renewed with the current settings. Otherwise polyhedra will only be built around atoms which are not yet central atoms of previously created polyhedra.

Design

Opens the Design for new polyhedra dialog, where you can define design, hatching, and surface properties of the polyhedra, which are to be created with this dialog.

Remarks

Please note that the filter function takes effect on the generation of coordination polyhedra, so that possibly some atoms are not taken as centers or ligands of coordination polyhedra, although the corresponding atom types are selected in the lists of Central atoms and Ligand atoms rsp.. See "Filter: Overview" about the filter function.

The generation of coordination polyhedra works with completed as well as incomplete coordination spheres. That means missing ligand atoms will be supplemented if necessary. Generic spheres are used to create ligand atoms which are bonded to the central atom. The dimensions of these spheres are defined in the connectivity list and vary thus from atom type pair to atom type pair. The polyhedra procedure does not generate ligand atoms that are selected in the list Ligand atoms but are not selected as bonded in the connectivity list. If fixed spheres are used, even such ligand atoms will be created that are not defined as bonded in the connectivity list.

See also:

Coordination Polyhedra: Overview


Design page (Edit polyhedra/Design for new polyhedra dialog)
Design

The Design page is part of the Edit polyhedra dialog or the Design for new polyhedra dialog.

Style

Defines what faces of the polyhedron are to be displayed as open or closed. Select one of the following options:

Open faces	All faces will be displayed open.
Front open	Back faces will be drawn closed, front faces open or closed. A face will be drawn transparent (open), if its normal vector encloses an angle less than the angle defined in Opening angle with the z-axis of the view coordinate system.
Closed faces	All faces will be displayed closed.

Opening angle

Defines the angle (in degrees) that decides whether a face will be displayed open or closed. This value is relevant only if the Style is set to Front open.

Interior

Defines the color and brush to fill the polygons that represent the polyhedron faces. Color defines the color, whereas Brush defines, if and how the interior is filled. See the article "Coordination Polyhedra: Designs" about polyhedron designs.

Use central atom's main color as interior color

If this checkbox is checked, the Color combobox is not available, and the main color of the polyhedron's central atom will be used as interior color. The main color is derived from the central atom's design: The main color is the interior color of an atom If the atom is hollow or has black or white as interior color, Diamond takes the edge color instead.

Edge

Defines the color, pen, and thickness of the polyhedron faces' edges. Color defines the color, whereas Pen defines, if and how the edge is drawn. Thickness defines the thickness of a solid edge in millimeters. See the article "Coordination Polyhedra: Designs" about polyhedron designs.

Rendered

If this checkbox is checked, rendering is used for the polyhedron preview.

Save as default

If this checkbox is checked, the settings in this dialog will be saved in the Diamond configuration, and will hereafter be used as default design for new polyhedra.

Options

Opens the Global settings for polyhedra dialog.

See also:

Coordination Polyhedra: Overview


Hatching page (Edit polyhedra/Design for new polyhedra dialog)
Hatching

The Hatching page is part of the Edit polyhedra dialog or the Design for new polyhedra dialog.

Style

Defines what faces are to be hatched:

No hatching	None of the faces will be hatched.
Front faces only	Front faces will be hatched but not back faces. This option is useful for either closed or front open polyhedra.
Back faces only	Back faces will be hatched but not front faces. This option is useful only for front open polyhedra, since only these enable a view to the back faces.
All faces	All faces will be hatched.

Distance

Defines the three-dimensional distance between the (parallel) hatching lines in Angstroems.

Vector

Defines the vector that determines the direction of the hatching lines. The three components of the vector refering to the reference coordinate system are defined in the input fields X, Y and Z.

Relative length for each hatching line

If this value is 1 (default value), the hatching lines touch the polyhedron edges. With a value between 1 and 0 these lines will be drawn shorter. E.g. with a value of 0.8, 10 percent at each end of the line will be omitted. This option may be used to contrast with the polyhedron edges.

Line style

Defines color, pen, and thickness of the hatching lines. Color defines the hatching color, whereas Pen defines, if and how lines will be drawn. Thickness defines the thickness of solid hatching lines in millimeters.

Rendered

If this checkbox is checked, rendering is used for the polyhedron preview.

Save as default

If this checkbox is checked, the settings in this dialog will be saved in the Diamond configuration, and will hereafter be used as default design for new polyhedra.

Options

Opens the Global settings for polyhedra dialog.

See also:

Coordination Polyhedra: Overview


Global settings for polyhedra dialog
Global settings for polyhedra

Defines settings which apply to all polyhedra and cannot be set individually to selected polyhedra.

Darken back faces

If this checkbox is checked, the back faces are drawn darker than front faces. This makes it easier to distinguish between front and back faces if polyhedra are particularly open.

Show internal bonds

If this checkbox is checked, bonds (as far as defined) between central atom and ligand atoms will be drawn. This setting is not useful for closed polyhedra.

Ligand atoms reducing factor

Defines a factor between 0.0 and 1.0 that reduces the radii of all atoms which are ligand atoms of any polyhedra. That means a value of 1 does not have any influence to the atoms' original sizes, whereas a value of 0 suppresses these atoms completely.

See also:

Coordination Polyhedra: Overview


How to Build Polyhedra

Selects the polyhedron building mode. This dialog appears if three or more atoms have been selected and one of the commands that build polyhedra has been called. Since Diamond does not know, if you want to build N polyhedra with the N selected atoms as centers or if you want to build one single polyhedron with the N selected atoms becoming corners, you have to decide between two building modes.

Use selected atoms as central atoms

If you choose this setting, the N selected atoms are considered as central atoms for N (new) polyhedra. This is the semi-automatic mode of creating polyhedra, where the corners of the new polyhedra derive from atoms within the enclosure sphere of the central atom. This enclosure sphere may either have fixed size or depend on the atom types of central atoms and coordinating atoms. (See the article "Coordination Polyhedra: Using Fixed or Generic Spheres" in the online user manual.) If necessary, these coordinating atoms will be created during the polyhedron creation process automatically.

Construct one single polyhedron from selected atoms

If you choose this setting, the N selected atoms are considered as corners of one single, new polyhedron. This is the manual mode of creation a polyhedron. The manual creation of a polyhedron has the advantage that you can create a polyhedron even for arbitrary environments, without regarding an enclosure sphere. After you confirm this dialog with OK, Diamond will propose a suitable atom in the center of the N selected atoms to become central atom of the new polyhedron, or you create a new (dummy) atom as center.

See also:

Coordination Polyhedra: Overview


Build Polyhedron

This dialog appears after you have selected three or more atoms, have called one of the polyhedron building commands and have chosen to construct one single polyhedron from the N selected atoms instead of creating N new polyhedra with the N selected atoms as centers.

Choose central atom...

This list contains all atoms, which can be created directly from the parameter list or by applying suitable symmetry operations to become central atom of the new polyhedron. For each atom, the atom symbol, the symmetry code and the distance of the atom from the center of the selected atoms (in Angstroems) is given. This value is usually zero for a "regular" polyhedron. If there is no suitable atom in the sphere (whose limits are given by the selected atom that is closest to the center), Diamond proposes the creation of a dummy atom. The option to choose a dummy atom instead of a real atom from the parameter list is available in any case. Diamond will add the selected atom automatically to the structure picture, if it has not yet been created.

Angle epsilon

Defines an angle used for the extension of triangular polyhedron faces to polygons with four or more edges. Diamond tries to extend the initially built triangular faces to polygons with four or more edges. For that, additional points are checked whether they are positioned approximately in the plane formed by the points of the triangle. If such a point encloses an angle of less than Angle epsilon degrees with the plane, it will be added to the triangle leading to a square, pentagon, etc. For details, see the article "Getting Polygons Greater Than Triangles".

Overwrite existing polyhedra

If this checkbox is checked, an existing polyhedron will be deleted and renewed with the current settings. Otherwise a polyhedron will only be built around an atom which is not yet central atom of a previously created polyhedron.

Design

Opens the Design for new polyhedra dialog, where you can define design, hatching, and surface properties of the polyhedron that is to be created with this dialog.

See also:

Coordination Polyhedra: Overview


Structure command (Display menu)

Opens the Display structure command, which defines global settings for the representation of the structure picture, such as:

- model,

- projection, camera distance, enlargement factor,

- settings for stereoscopic view,

- settings for rendered representation,

- settings for lighting and depth cueing,

- settings for emphasizing specific objects,

- the overall radius factor.

See also:

Display of Structure Picture: Overview


Standard page (Display structure dialog)
Standard

The Standard page is part of the Display structure dialog.

Model

Selects between wire, ball-and-stick and space-filling model:

Wire model	Displays only bonds between atoms as thin lines proportionately with both colors of the bonded atoms. Non-bonded atoms appear as thin points. For rendered representation, a variation of the wire model, called stick model, is available. See "Using Sticks Instead of Thin Wires" for details.
Ball-and-stick model	The default model and displays the atoms as spheres (or ellipsoids) and bonds as lines or tubes. Only this model enables the representation of coordination polyhedra and thermal ellipsoids.
Space-filling model	Displays only atoms (with their assigned van der Waals radii) but no bonds.

See "Models: Overview" for more information.

Projection

Selects between parallel and central projection. See "Projection: Overview" for more information.

Camera distance

Defines the distance between viewer (or the "camera") and the drawing area or the screen, rsp. More exactly it is the distance between the current center of rotation of the structure and the viewers' position on the z-axis of the view coordinate system. The distance is given in centimeters (cm). The perspective impression is the stronger the lower this distance is set. Additionally a big enlargement factor contributes to this impression, because the distance is defined in cm and thus depends on the enlargement factor. In extreme cases, i.e. if objects are positioned on a level with the viewer or even behind him, the drawing of these objects will be suppressed. For a perspective impression the radio button central must be switched on. For details, see "Viewing Distance".

Enlargement factor

Defines the enlargement factor (in centimeters per Angstroem). If central projection is used, this value refers to the z position of the center of rotation. Then objects nearer than the center are represented bigger, but those behind smaller. For details, see "Enlargement Factor" and "Distortion of Atoms and Bonds".

Stereo

Represents the structure in stereoscopic view, if enabled is checked. The stereoscopic view consists of two pictures of the same structural part. The distance between these pictures (exactly: the distance between the two projections of the center of rotation) is given in Pictures' distance in centimeters. Stereo angle defines the value (in degrees) that is used to twist the pictures

against each other along the y-axis of the view coordinate system. For details, see "Stereo Representation".

Depth cueing

Makes objects brighter or darker dependent from the object's "depth", i.e. the z-value (in view coordinates), if enabled is checked. Intensity defines the intensity of this effect in RGB units per Angstroem. Each RGB value (red, green, blue) has a range from 0 through 255. For positive values the front objects are brighter, for negative values darker instead. For details, see "Depth Cueing".

Shading edge

Defines if and how to draw a shading edge around each atom and bond to bring them out from other objects in the rear. The thickness of the line used to draw the shading edge is given in millimeters. The background color is used for this edge. Set this value to zero, if you do not want any shading edges. For details, see "Shading Edge".

Front emphasizing

Defines a value to enlarge the width of the edges of atoms, bond tubes, polyhedra etc. This value is given in millimeters (mm) and is added to the generic width of the edges. The front emphasizing value refers to the most front object of the picture and is interpolated for all objects with z > 0 between 0 and this value. The edges of objects with z < 0 leave unchanged. For details, see "Front Emphasizing".

Bond tapering factor

Distorts thick bonds, which are displayed as tubes, for a better impression of depth. For a value greater than 0, cylindric tubes are distorted to tapers with the thicker end in the front. In the extreme case, i.e. the tube is parallel to the z-axis and the bond tapering factor is 1 (or higher), the taper becomes a cone. Tapering factors higher than 1 may be used to distort even bonds at acute angles to the drawing area to cones. For details, see "Bond Tapering".

Overall radius factor

Defines a factor all atomic radii are multiplied with - but only in the ball-and-stick model. The default value is 1. For details, see "Overall Radius Factor".

Black-on-white mode

If this checkbox is checked, the background is painted (screen) or remains (printout) white. Otherwise the background color (see below) is used. In black-on-white mode the color "Auto" is set to black, else to white. See "Background: Overview" for more information.

Background color

Opens the MS Windows standard dialog Color to select a color value for the background color. This color will be ignored if Black-on-white mode is checked.

See also:

Display of Structure Picture: Overview


Rendering page (Display structure dialog)
Rendering

The Rendering page is part of the Display structure dialog.

Rendered representation of structure picture

If this checkbox is checked, the structure picture will be represented rendered. Otherwise, flat representation will be used.

Wire model options

Defines how "wires" are represented in the wire model with rendered representation:

Lines	"Wires" are drawn as lines like in flat representation. Since these lines are no tubes, that means no 3D objects, these lines are not shaded.
Sticks	"Wires" are drawn as tubes with a radius given in Radius in Angstroems. These tubes are 3D objects and will thus be shaded.

Superimpose space-filling model

Defines if and how a space-filling model shall be drawn over the regular wire or ball-and-stick model. For details, see "Superimposition of Space-Filling Model".

No superimposing	No additional space-filling-model will be drawn over the regular wire or ball-and-stick model.
Transparent	An additional space-filling-model will be drawn over the regular wire or ball-and-stick model with transparent spheres. The transparency is given in Factor, which has a range of 0 to 1. With a factor of zero, the space-filling model keeps invisible, with 1 it is opaque (not transparent).
Opaque	The additional space-filling model will be drawn with non-transparent spheres.

Resolution of atoms

In rendered representation, an atom (ellispoid) is drawn as a (distorted) sphere of a given radius centered around the origin. The sphere is subdivided around the z-axis into slices and along the z-axis into stacks (similar to lines of longitude and latitude). The resolution that is defined here specifies the number of subdivisions around the z-axis (similar to lines of longitude) and the number of subdivisions along the z-axis (similar to lines of latitude).

Automatic, high	The resolution varies with the real size of the sphere and is relative high.
Automatic, low	The resolution varies with the real size of the sphere and is relative low.
Fixed	The resolution is independent from the real size of the sphere and is defined by the value given in the input field.

Resolution of bonds

In rendered representation, a bond is drawn as a cylinder. Like a sphere, a cylinder is subdivided around its axis into slices, and along its axis into stacks. The resolution that is defined here specifies the number of subdivisions around the z-axis. The settings have the same meaning as for Resolution of atoms.

See also:

Rendered Representation: Overview


Lighting page (Display structure dialog)
Lighting

The Lighting page is part of the Display structure dialog.

Enable lighting

If this checkbox is checked, lighting is enabled for both flat and rendered representation.

Standard intensity

Defines the intensity of lighting only for flat representation. This value takes no effect on rendered representation. (The composition of the directional light source which is used for rendered representation, is defined in Ambient/Diffuse/Specular light component.)

With a value of 0, no lighting is used, whereas 1 leads to maximum intensity. Diamond's lighting value is an empiric value:

a) Atoms get a lighting bulb if the intensity lies between 0 and 0.5 with a color interpolated between the atom's main color (0.0) and white (0.5). For values higher than 0.5 the bulb is white too. Note: Thermal ellipsoids will never be lighted.

b) A polyhedron face appears white if the intensity is 1.0 and the light falls on it orthogonally. Faces on the opposite side of the light source appear black. For lower intensities and non-orthogonal light falls, the color is interpolated between the faces' main color and white or black rsp.

Light source vector

X, Y, and Z define the three components (x,y,z) in view coordinates of the lighting vector. This vector points from the center of rotation towards the light source. If the vector is set to (-1, 1, 1) e.g., the light comes from the upper left front.

Ambient light component

Defines the red, green, and blue component of the ambient light component of the directional light. For details, see "Lighting Effects for Rendered Representation". These settings take no effect on flat representation.

Diffuse light component

Dito for diffuse component of the directional light.

Specular light component

Dito for specular component of the directional light.

See also:

Lighting: Overview

Rendered Representation: Overview


Adjust command (Display menu)

Opens the Adjust dialog where you can define the size of the border which is used for manual or automatic adjustment of the structure to the window or page size. The dialog is also used to enable or disable automatic adjustment.

See also:

Adjusting the Structure


Adjust direct command (Display toolbar)

Adjusts the structure picture to the current size of the structure window or the size of the page, if Diamond is in page view mode (see "Page View: Overview"). The size of the border, which is used for adjusting can be changed in the Adjust dialog, which is opened from the Adjust command in the Display menu.

See also:

Adjusting the Structure


Adjust dialog
Adjust

Defines the size of the border which is used for manual or automatic adjustment of the structure to the window or page size. The dialog is also used to enable or disable automatic adjustment.

Horizontal border

Defines the border in centimeters which is used on both the left and right side of the page or structure window when the structure is adjusted.

Vertical border

Defines the border in centimeters which is used on both the upper and lower side of the page or structure window when the structure is adjusted.

Automatic adjustment

If this checkbox is checked, the structure is adjusted whenever it is redrawn or whenever the size of the structure window or page changes.

See also:

Adjusting the Structure


View command (Display menu)

Opens the View dialog to define a view along a selected axis.

See also:

Viewing Along Selected Axes


View dialog
View

Defines a view along a specific axis.

View along axis

When pushing one of the six pushbuttons a, b, c, x, y or z, the structure will be oriented in this way that the vector a, b or c of the unit cell or the x-, y- or z-axis rsp. of the reference coordinate system points towards you.

Opposite direction

If this checkbox is checked, the selected axis points away from you instead towards you.

View along special axis

Defines a vector with components u, v, w referring to the crystal coordinate system (input fields u, v, and w) that will be projected to the z-axis of the view coordinate system, that means it will point towards you, after the Set button of this group is pushed.

View towards plane

Defines a plane parallel to the xy-plane of the view coordinate system, that means the plane of the drawing or printing area. The input fields h, k, and l contain the Miller indexes of this plane. The orientation will be set after the Set button of this group is pushed. Integer numbers may be used as well as non-integer numbers for h, k, and l. The Miller indexes of the plane derived from the current orientation are given below the input fields.

Define axis

Closes this dialog and lets you select two atoms #1 and #2. An axis is defined between these two atoms. The center of rotation will be set into atom #1. The structure will then be oriented in this way that the axis to atom #2 points towards you.

Save view as standard orientation

If this checkbox is checked, the latest set viewing direction will be saved as standard orientation for new structure pictures (i.e. new or imported structures). E.g. if the button a is pushed and then this dialog closed, all new structures have the a-axis pointing towards you as default orientation. The Reset orientation command will let the a-axis point towards you, too.

See also:

Viewing Along Selected Axes

Viewing Towards a Plane Given By Miller Indexes h,k,l


Center of rotation command (Display menu)

Opens the Center of rotation dialog, where you can change the center of rotation and enable or disable automatic centering.

See also:

Center of Rotation


Center of rotation dialog
Center of rotation

Defines the center of rotation and enables or disables automatic centering.

Center of rotation at position

X, Y, and Z define the current center of rotation either in crystal or reference coordinates, depending on the setting in Coordinate system. (For the center of rotation, view and reference coordinates are identical.)

Coordinate system

Defines the coordinate system, which X, Y, and Z refer to.

New position

Defines the new center of rotation. The center of rotation will be set when closing the dialog with OK.

as stated above	accesses the values in X, Y, and Z as new center of rotation.
center of selected atoms	defines the position of the selected atom (if one atom has been selected) or the center of the selected atoms as new center of rotation. The values in X, Y, and Z will not be taken into account.
center of gravity	defines the center of all created atoms as new center of rotation. The values in X, Y, and Z will not be taken into account.

Consider cell edges for centering

If this checkbox is checked, the center of all created atoms including cell corners will become the new center of rotation, when center of gravity is selected in New position. Otherwise only atoms are taken into account.

Automatic centering

If this checkbox is checked, the center of rotation is changed automatically after every operation that builds up or destroys structural parts. The automatic centering behaves like defining a new center of rotation manually with the center of gravity option in New position.

See also:

Center of Rotation


Center of rotation command (Display toolbar)

Defines the position of the selected atom (if one atom has been selected) as new center of rotation. If multiple atoms have been selected, the center of the atoms will be taken as new center of rotation. If no atom has been selected, the center of all created atoms will be taken instead. In the latter case, cell corners may be taken into account depending on the settings in the Center of rotation dialog, which can be opened from the Center of rotation command in the Display menu.

See also:

Center of Rotation


Center+Adjust command (Display toolbar)

Performs centering and adjusting of the current structure in one step.

First step: Centering

Defines the position of the selected atom (if one atom has been selected) as new center of rotation. If multiple atoms have been selected, the center of the atoms will be taken as new center of rotation. If no atom has been selected, the center of all created atoms will be taken instead. In the latter case, cell corners may be taken into account depending on the settings in the Center of rotation dialog, which can be opened from the Center of rotation command in the Display menu.

Second step: Adjusting

Adjusts the structure picture to the current size of the structure window or the size of the page, if Diamond is in page view mode (see "Page View: Overview"). The size of the border, which is used for adjusting can be changed in the Adjust dialog, which is opened from the Adjust command in the Display menu.

See also:

Center of Rotation

Adjusting the Structure


Zoom command (Display toolbar)

Zooms a rectangular area of the structure window to the current size of the window. The enlargement factor will be increased and the position of the structure moved so that the rectangular area fits optimally within the structure window.

After you have chosen this command, the mouse cursor changes to a special symbol symbolizing a dotted rectangle. Then perform the following steps:

1. Move the mouse cursor to the upper left corner of the desired area.

2. Press the left mouse button down and move the mouse cursor (with mouse button still down!) to the lower right corner of the desired area.

3. Release the mouse button. After that the structure will be enlarged and re-positioned.

See also:

Zooming a Rectangular Area


Orientation command (Display menu)

Opens the Orientation dialog to define the orientation of the structure as well as the position within the structure window.

See also:

Orientation and Position


Orientation dialog
Orientation

Defines the orientation of the structure as well as the position within the structure window.

Angles of rotation along axes

X, Y, and Z define the angles along the x-, y- and z-axis (in this order) the structure must be rotated from the basic orientation. Basic orientation means the orientation where the axes of both reference and view coordinate system are identical. The angles are given in degrees.

Center of rotation...

X and Y define the horizontal and vertical position of the projection of the center of rotation relative to the center of the drawing area. The values are given in centimeters (cm), whereas positive values shift right and up rsp.

Reset

Resets all values to zero.

See also:

Orientation and Position


Reset orientation command (Display menu)

Rotates the structure back to its default orientation. Usually the axes of the view coordinate system are identical to those of the reference coordinate system, that means the x-axis points right, the y-axis up and the z-axis towards you. This default orientation may be changed by switching on the setting Save view as standard orientation in the View dialog, which can be opened with the View command in the Display menu, and setting the view along an axis other than the z-axis.

See also:

Orientation and Position


Rotate command (Display menu)

Opens the Rotate structure dialog which rotates the structure along the axes of the view coordinate system for discrete increments.

See also:

Rotating and Shifting the Structure


Rotate structure dialog
Rotate structure

Rotates the structure along the axes of the view coordinate system for discrete increments.

X-axis, Y-axis and Z-axis

Define the increments (in degrees) the structure is to be rotated along the x-, y- and z-axis (in this order) of the view coordinate system.

Apply

Performs the rotation without closing the dialog.

See also:

Rotating and Shifting the Structure


Shift structure command (Display menu)

Opens the Shift structure dialog which shifts the structure (exactly: the projection point of the rotational center) within the structure window (drawing area).

See also:

Rotating and Shifting the Structure


Shift structure dialog
Shift structure

Shifts the structure (exactly: the projection point of the rotational center) within the structure window (drawing area).

Horizontally, Vertically

Define the increments (in centimeters, cm) the projection point of the rotational center is shifted horizontally/vertically within the structure window. Positive values shift to the right and up rsp.

Apply

Performs the shift without closing the dialog.

See also:

Rotating and Shifting the Structure


Color differentiation command (Display menu)

Opens the Color differentiation dialog, which enables an alternative assignment of colors to the atoms. There are options to differentiate for:

- the charge or oxidation number,

- the site occupation factor,

- the number of the symmetry operation used to create an atom,

- the number of the Bravais translation used,

- the affiliation to (a) specific cell(s).

Additionally you may specify how to represent atoms on mixed sites.

See also:

Color Differentiation: Overview


Color differentiation dialog (Display menu)
Color differentiation

Enables an alternative assignment of colors to the atoms. There are options to differentiate for:

- the charge or oxidation number,

- the site occupation factor,

- the number of the symmetry operation used to create an atom,

- the number of the Bravais translation used,

- the affiliation to (a) specific cell(s).

Additionally you may specify how to represent atoms on mixed sites.

Criteria of differentiation

Defines what the color is to be differentiated for:

Standard	This is the default, where all atoms have their "own" design.
Charges/Oxidation numbers	The colors are differentiated for (formal) oxidation states or charges. There are 13 states for the oxidation numbers -4 through +8. The charge or (formal) oxidation number is rounded to an integer.
Site occupation factors	The colors are differentiated for site occupation factors. There are 10 ranges (0.0 .. 0.1; 0.1 .. 0.2; .....; 0.9 .. 1.0) plus the differentiation for 1.0.
Symmetry operations	The number of the symmetry operation (1 through a maximum of 48, depending on the current space group) is used to differentiate.
Bravais translations	The number of the Bravais translation (1 through a maximum of 4, depending on the centering of the current space group) is used to differentiate.
Cell translations	The atoms of a cell or a cell range can be emphasized.

Edit colors

The pushbuttons Oxidation numbers, Site occupations, Symmetry operations, Bravais translations and Cell translations open the dialogs to edit the color values of the corresponding differentiations.

Mixed sites representation

Defines if and how to differentiate atoms on mixed sites. The colors for multiple (trace) elements are defined with their corresponding atom types. See the article "Definition of Colors for Mixed Site Representation" how to assign these colors.

Representative only	This is the default setting. The atom which represents the site will be drawn using its "own" design.
Mix colors	The colors of all atoms on the site will be mixed according to their relative site occupations.
Sectors	The relations of the site occupations will be represented as a kind of pie diagram.
Concentric disks	The distribution will be represented as concentric disks with radii relative to the site occupations.

See also:

Color Differentiation: Overview


Color settings dialog
Color settings

Defines the colors for a selected color differentiation.

In the first list, the criterion to be differentiatied for can be selected, e.g. an oxidation state.

In the second list, the corresponding color can be selected.

See also:

Color Differentiation: Overview


Color settings dialog (cell range)
Color settings

Defines the two colors for atoms belonging to an emphasized cell range as well as for the rest.

Range

Selects the range, which the color in the color combobox below is to be assigned to.

Color

Defines the color for the range, which has been selected in the Range list.

Dimensions of highlighted range

Define the codes for integer cell translations, where the upper triple of digits defines the lower, the lower triple the upper bound of the emphasized range. These triples are the XYZ values of the atom code (general form: AXYZSSB) used by Diamond. XMin and XMax define the bounds for integer cell translations along the a-axis of the unit cell, whereas YMin and YMax are the corresponding values for the b-axis, and ZMin and ZMax the values for the c-axis. If zero is given in all six input fields, all atoms will be highlighted that have been generated without any integer cell translation.

Note: Since the coordinates of the atoms of the parameter list do not necessary have standardized values from 0 to 1, these atoms need not necessarily be positioned within the unit cell.

See also:

Color Differentiation: Overview


Hide command (Display menu)

Opens the Hide dialog, where you can hide objects of selected types, e.g. atoms, coordination polyhedra, etc. Please note that the objects are only hidden, but not removed. That means the hidden objects will be stored in the Diamond structure files and will re-appear when the structure picture will be loaded at a later time.

See also:

Selecting Objects

Displaying Polyhedra With Front Faces Open


Hide dialog
Hide

Hides objects of selected types, e.g. atoms, coordination polyhedra, etc. Please note that the objects are only hidden, but not removed. That means the hidden objects will be stored in the Diamond structure files and will re-appear when the structure picture will be loaded at a later time.

Hide all atoms

If this checkbox is checked, all created atoms will be hidden. This does not hide bonds connected to these atoms.

Hide all bonds

If this checkbox is checked, all bonds between created atoms will be hidden.

Hide all cell edges

If this checkbox is checked, all cell edges will be hidden. This takes no effect on the display of the unit cell axes a, b, and c.

Hide all polyhedra

If this checkbox is checked, all coordination polyhedra will be hidden.

Hide front faces of all polyhedra

If this checkbox is checked, the front faces of all polyhedra will not be drawn. This enables to view insight polyhedra and to select the central atoms easier.

Hide all atom labels

If this checkbox is checked, all atom labels will be hidden. This makes it easier to select atoms that are "covered" by their labels.

Hide all bond labels

If this checkbox is checked, all bond labels will be hidden. This makes it easier to select bonds that are "covered" by their labels.

Hide user-defined text

If this checkbox is checked, all user-defined text will be hidden.

Display all

Resets all hidden states, and closes the dialog.

See also:

Selecting Objects

Displaying Polyhedra With Front Faces Open


Grid command (Display menu)

Opens the Grid dialog, which enables the display of a grid, which may be helpful for the positioning of objects like text etc.

See also:

Grid


Grid dialog
Grid

Enables the display of a grid, which may be helpful for the positioning of objects like text etc.

Display grid

The grid will only be displayed if this checkbox is checked.

Unit

Defines the unit as well as the distance between the lines of the grid. Possible units are Angstroem and Centimeters. The corresponding distance values are defined in Delta. The distance depends on the current enlargement factor if defined in Angstroem. If central projection is used, this is the distance for z=0, i.e. on the z level of the rotational center.

Origin

Defines the origin of the coordinate system of the grid. In all cases the scale points to the right and up.

Left bottom	The origin is in the lower left corner of the structure window or the page, if page view mode is active.
Window center	The origin is in the center of the structure window or the page, if page view mode is active.
View Coordinate's System origin	The origin is identical with the projection of the center of the rotation in the structure window or on the page. Thus the grid origin moves with the center of rotation, if the structure is shifted.

Remark

The grid appears only on the screen and will never be printed or written to a metafile.

See also:

Grid


Grid on/off command (Display toolbar)

Switches the grid on or off, which may be helpful for the positioning of objects like text etc.

If you want to change the settings, e.g. the dimensions of the grid, you must open the Grid dialog via the Grid command in the Display menu.

See also:

Grid


Open polyhedron faces command (Display toolbar)

Temporarily hides the front faces of all coordination polyhedra. This enables to view insight polyhedra and to select the central atoms easier.

See also:

Displaying Polyhedra With Front Faces Open


Page view command (Display menu)

Toggles between normal and page view mode.

If the page view modehas been activated, the entire (printout) page will be represented within the structure window - independent from the window’s actual size. The page format may be changed via the Print setup command in the File menu. Diamond changes to black-on-white mode, if the setting Print black on white in the Print page of the Options dialog is active.

See also:

Page View: Overview


Toolbars command (Display menu)

Opens the Toolbars dialog, where you can select the toolbars to be displayed. Additionally you can enable or disable tooltips.

See also:

Toolbars


Toolbars dialog
Toolbars

Selects the toolbars to be displayed. Additionally you can enable or disable tooltips.

Standard toolbar

If this checkbox is checked, the standard toolbar is displayed. This toolbar contains the standard symbols for "New", "Open", "Print", "Copy", "Undo", etc.

Build toolbar

If this checkbox is checked, the Build toolbar is displayed. This toolbar contains symbols for functions which build up or destroy a structure picture, such as "Fill Unit Cell", "Molecules", etc.

Display toolbar

If this checkbox is checked, the Display toolbar is displayed. This toolbar contains symbols for displaying functions.

Tracking toolbar

If this checkbox is checked, the Tracking toolbar is displayed. This toolbar contains symbols to switch between tracking modes.

Measure toolbar

If this checkbox is checked, the Measure toolbar is displayed. This toolbar contains symbols for the interactive measuring of distances and angles.

Display Tool tips

If this checkbox is checked, tooltips appear when the mouse cursor touches a button in a toolbar.

See also:

Toolbars


Data sheet command (Display menu)

Activates the data sheet. The data sheet will be displayed in the secondary pane of the structure window.

See also:

Panes

Data Sheet: Overview


Distances and angles command (Display menu)

Activates the list of distances and/or angles. This list will displayed in the secondary pane of the structure window.

See also:

Panes

Distances and Angles: Overview


List atomic parameters command (Display menu)
List | atomic parameters command (Display menu)

Activates the list of atomic parameters. This list will displayed in the secondary pane of the structure window.

See also:

Panes

Atomic Parameters


List created atoms command (Display menu)
List | created atoms command (Display menu)

Activates the list of created atoms. This list will displayed in the secondary pane of the structure window.

See also:

Panes

Created Atoms


List bonds command (Display menu)
List | bonds command (Display menu)

Activates the list of created bonds. This list will displayed in the secondary pane of the structure window.

See also:

Panes

Created Bonds


List atom types command (Display menu)
List | atom types command (Display menu)

Activates the list of atom types. This list will displayed in the secondary pane of the structure window.

See also:

Panes

Atom Types


List bond types command (Display menu)
List | bond types command (Display menu)

Activates the list of bond types. This list will displayed in the secondary pane of the structure window.

See also:

Panes

Bond Types


List polyhedra command (Display menu)
List | polyhedra command (Display menu)

Activates the list of coordination polyhedra. This list will displayed in the secondary pane of the structure window.

See also:

Panes

Coordination Polyhedra: Overview


Wire model command (Display toolbar)

Selects the wire model.

See also:

Models: Overview


Ball-and-stick model command (Display toolbar)

Selects the ball-and-stick model, which is Diamond's regular model.

See also:

Models: Overview


Space-filling model command (Display toolbar)

Selects the space-filling model.

See also:

Models: Overview


Perspective command (Display toolbar)

Switches between parallel (toolbar button up) and central projection (down).

See also:

Projection: Overview


Depth cueing command (Display menu)
Depth cueing command (Display toolbar)

Enables (toolbar button down) or disables depth cueing.

See also:

Depth Cueing


Lighting command (Display menu)
Lighting command (Display toolbar)

Enables (toolbar button down) or disables lighting.

See also:

Lighting: Overview


Stereo command (Display toolbar)

Enables (toolbar button down) or disables stereo representation.

See also:

Stereo Representation


Axes a, b, c command (Display toolbar)

If the toolbar button is down, the unit cell axes a, b, c will be displayed in the structure picture.

See also:

Displaying the Unit Cell Axes


Ellipsoids command (Display toolbar)

Enables (toolbar button down) or disables the display of thermal ellipsoids instead of spheres, if valid anisotropic displacement parameters have been defined.

See also:

Thermal Ellipsoids: Overview


Rendering command (Display toolbar)

If the toolbar button is down, the structure picture is drawn with rendered representation. Otherwise flat representation is used.

See also:

Rendered Representation: Overview


Info mode command (Tools menu)

Switches to the info mode or ends the info mode, if this mode has yet been activated.

In info mode, the mouse cursor changes to an arrow with the letter "i". The modeless Object info window will be opened to display informations about a selected object. The kind of information depends on the object type (atom, bond, text, etc.).

You can further end the info mode by closing the Object info window or with the Escape key.

See also:

Info Mode: Overview


Distances command (Tools menu)

Switches to the measure mode, which measures distances between two selected atoms, or ends the measure mode, if this mode has yet been activated.

In this kind of measure mode, the mouse cursor changes to an arrow with a ruler symbol. The modeless Distances window will be opened to display previously measured distances. New distances will be appended to this list.

You can further end the measure mode by closing the Distance window or with the Escape key.

See also:

Distances and Angles: Overview


Angles command (Tools menu)

Switches to the measure mode, which measures angles between three selected atoms, or ends the measure mode, if this mode has yet been activated.

In this kind of measure mode, the mouse cursor changes to an arrow with an angle symbol. The modeless Angles window will be opened to display previously measured angles. New angles will be appended to this list.

You can further end the measure mode by closing the Angles window or with the Escape key.

See also:

Distances and Angles: Overview


Torsion angles command (Tools menu)

Switches to the measure mode, which measures torsion angles between four selected atoms, or ends the measure mode, if this mode has yet been activated.

In this kind of measure mode, the mouse cursor changes to an arrow with an angle symbol. The modeless Torsion angles window will be opened to display previously measured angles. New angles will be appended to this list.

You can further end the measure mode by closing the Torsion angles window or with the Escape key.

See also:

Distances and Angles: Overview


Object info window
Object info

This modeless window displays infos about the selected object (atom, bond, text, etc.).

Close

Closes the window and ends the object info mode.

Copy

Copies the selected lines from the list to the clipboard.

Informations about a selected atom

Atom no.	Defines the index of the created atom in the list of created atoms. The first index is zero.
Symbol	Symbol of the atom of the parameter list, where the created atom has been derived from.
Chemical composition	Element symbol (plus attached hydrogen atoms as far as defined), followed by the oxidation number in parentheses (as far as defined). If the site occupation factor is defined but not 1, this factor follows the symbol. If the created atom is on a mixed site, element symbols, oxidation numbers and site occupation factors of all atoms on the mixed site will be enumerated.
Atom type	The symbol of the associated atom type.
Original coordinates	The fractional coordinatesref_coord of the atom in the parameter list, which the created atom has been derived from.
Atom code (no., symmetry)	The atom code of the created atom and (in parentheses) zero-based index of the atom from the parameter list as well as the symmetry operation that generated the atom.
Crystal coordinates	The crystal coordinates of the created atom.
Reference coordinates	The reference coordinates of the created atom.
View coordinates	The view coordinates of the created atom.

Informations about a selected bond

Bond no.	Defines the zero-based index of the bond in the list of created bonds.
Atom symbols	Symbols of the atoms of the parameter list, where the created atoms which are connected with this bond, have been derived from.
Atom code 1 (no., symmetry)	The atom code of the first created atom which is connected with the second atom, and (in parentheses) zero-based index of the atom from the parameter list as well as the symmetry operation that generated the atom.
Atom code 2 (no., symmetry)	dito for the second atom.
Bond length	The bond length, given in Angstroems.

Informations about a selected atom label

Atom label no.	Defines the zero-based index of the atom label in the atom label list.
Label text	The contents of the atom label.
Label size	The size in Angstroems of the label.
Label position (x, y, z)	The 3D position of the label relative to the center of the associated atom.
Atom no.	The zero-based index of the associated atom in the list of created atoms.
Symbol	The symbol of the atom of the parameter list, where the associated atom has been derived from.

Informations about a selected bond label

Bond label no.	Defines the zero-based index of the bond label in the bond label list.
Label text	The contents of the bond label.
Label size	The size of the label in Angstroems.
Label position (x, y, z)	The 3D position of the label relative to the center of the associated bond (this is the centerpoint of the two connected atoms).
Bond no.	The zero-based index of the associated bond in the list of created bonds.
Atom symbols	The symbols of the atoms of the parameter list, where the associated atoms has been derived from, which are connected with the associated bond.

Informations about a selected text

User-defined text no.	The zero-based index of the text in the list of user-defined text strings.
Content	The contents of the text string.
Text size	The size of the text in centimeters.
Text position	The position of the leftmost point of the baseline of the text relative to the structure windows's or page's center, in centimeters.

Information about the coordinate system or legend of atom types

If coordinate system or legend of atom types have been selected, the position relative to the reference point in centimeters as well as the reference point itself are given.

See also:

Info Mode: Overview


Distances/Angles/Torsion angles dialog
Distances/Angles/Torsion angles

This modeless window displays informations about previously or actually defined distances, angles, or torsion angles.

Copy

Copies the selected lines to the clipboard.

Delete

Removes the selected lines from the list of measured or reported distances, angles, or torsion angles, rsp.

Done

Closes the window and ends the measure mode.

Informations about each reported or measured distance

Atom #1	The symbol of the first atom. The symbol comes from the atomic parameter list.
Atom #2	Dito for the second atom.
SymmCode	The symmetry code of the second atom. The symmetry code for the first atom is "x,y,z" in any case.
Dist.	The distance between atom #1 and atom #2 in Angstroems.

Informations about each reported or measured angle

If three atoms #1, #2, and #3 are clicked one after the other, atoms #1 and #3 define the two atoms at the sides of the angle.

Atom #1	The symbol of atom #1. The symbol comes from the atomic parameter list.
SymmCode	The symmetry code for atom #1.
Atom #2	The symbol of atom #2. No symmetry code will be given for atom #2, since the symmetry code for this atom is "x,y,z" in any case.
Atom #3	The symbol of atom #3.
SymmCode	The symmetry code for atom #3.
Angle	The angle at atom #2, between the atoms #1 and #3, given in degrees.

Informations about each reported or measured torsion angle

The torsion angle is calculated as described in Klyne, W. & Prelog, V. (1960), Experientia, 16, 521. The vector direction from atom #2 to atom #3 is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector from atom #2 to atom #1 onto the projection of the vector from atom #3 to atom #4. Clockwise torsions are positive, counterclockwise torsions are negative.

Atom #1	The symbol of atom #1. The symbol comes from the atomic parameter list.
Atom #2	The symbol of atom #2.
Atom #3	The symbol of atom #3.
Atom #4	The symbol of atom #4.
Angle	The torsion angle, given in degrees.

See also:

Distances and Angles: Overview


Auto format command (Tools menu)

Opens the Auto format dialog, which offers several options to optimize the representation of the structure picture for several purposes.

See also:

Optimizing the Representation of the Structure Picture: Overview


Auto format dialog
Auto format

Offers several options to optimize the representation of the structure picture for several purposes.

Destination

Defines how the structure picture is to be changed:

Rendered representation (highest quality)	Switches to rendered representation, activates lighting and depth cueing. Switches black-on-white mode off.
Light bulb representation on dark background	Uses flat representation, activates lighting (for the light bulbs) and depth cueing. Switches black-and-white mode off.
Flat colored objects on dark background	Uses flat representation. Switches lighting, depth cueing, and black-and-white mode off.
Flat colored objects with black edges on white background	Uses flat representation. Switches lighting and depth cueing off. Switches to black-and-white mode. The designs of atoms, thick bonds, and polyhedron faces are adjusted to have black edges for a better contrast on white background.
Gray-scaled objects on white background	Works like the previous option, but all lines will become black, and all filling colors converted to gray-scales.
Pure black-and-white representation on white background	Works like the previous option, but all atoms, thick bonds, and polyhedron faces will not be filled (that means they have white interior).

Update atom type designs

Some of the options mentioned above change the designs of the created atoms. If this checkbox is checked, the designs of the atom types will be changed, too.

Update bond type designs

Some of the options mentioned above change the designs of the created bonds. If this checkbox is checked, the designs of the bond types will be changed, too.

Update standard polyhedron design

If this checkbox is checked, the default design for coordination polyhedra will be adjusted, if necessary.

See also:

Optimizing the Representation of the Structure Picture: Overview


Rock'n'Roll command (Tools menu)

Opens the Rock'n'Roll dialog, which may start a continuous rotation of the structure.

If this command is called from the Tracking toolbar, instead, the Rock'n'Roll dialog will not be opened, and the continuous rotation is started or halted.

See also:

Continuous Rotation ("Rock and Roll")


Rock'n'Roll dialog
Rock'n'Roll

Defines settings for continuous rotation along one through three axes.

Speed of rotation in deg/s

Defines the rotational speeds refering to the three axes x, y, and z of the view coordinate system in degrees per second (input fields x-axis, y-axis, z-axis). If multiple axes are selected (that means the corresponding angle in the input field is not zero), the rank order of axes during rotation is x, y, z.

Rocking around axes

Defines if the rotation should change its direction for a selected axis.

Border angles

Defines a lower and an upper bound in the two input fields. If the continuous rotation reaches one of these angle values, the direction of the rotation refering to the axis selected in Rocking around axes is reversed.

See also:

Continuous Rotation ("Rock and Roll")


Options command (Tools menu)

Opens the Options dialog, which defines several settings for tracking, stepping, as well as automatic saving, double buffering, etc.


Desktop page (Options dialog)
Desktop

The Desktop page is part of the Options dialog.

Double buffering

If this checkbox is checked, DIAMOND writes all drawings first into memory ('bitmap') and then copies the complete bitmap into the structure window. Otherwise, DIAMOND writes all output direct into the structure window.

For more details about double buffering, see the article "Double Buffering: Overview".

Refuse screen saving

If this checkbox is checked, DIAMOND refuses the MS Windows system message that tries to activate screen saving. In other words: Screen saving will not work while DIAMOND is running. Otherwise, screen saving will be performed as defined for the MS Windows system on your computer.

Print black on white

If this checkbox is checked, DIAMOND prints a structure picture as if the setting Black-on-white mode were activated in in the Structure display dialog that can be opened with the Structure command in the Display menu. Otherwise, the background color is used when printing, i.e. if you have defined a black background, most parts of your paper get black !!

See also the article "Printing, Copying, and Saving the Structure Picture: Overview" in the online user manual.

Size of print buffer

Defines the size (in kilobytes) of the internal buffer that Diamond will use to print a rendered picture. This value will be ignored for printing in standard mode. For details, see the article "Banding of Rendered Pictures" in the online user manual.

Auto Save

If this checkbox is checked, DIAMOND makes copies of all open structure documents as far as they are modified. These files can be used to restore structure documents, which have been left due to a system crash or caused by an improper exit of DIAMOND. See also: "Auto Save Function".

Interval

Defines the interval for Auto Save in minutes.

Open empty structure window when starting

If this checkbox is checked, Diamond opens an empty structure window every time it is started. (An empty structure window is what you can create manually using the New command from the File menu.). Otherwise, no structure window is displayed, unless a file name has been specified in the command line or another shell command. See the articles "Opening and Closing of Structure Windows" and "New Structure Window" for more informations.


Tracking page (Options dialog)
Tracking

The Tracking page is part of the Options dialog and defines the increments for the mouse-controlled rotation, shifting and zooming of structures (called "Tracking"), in other words, the ratio of e.g. rotational speed and mouse speed.

Degrees along ...axes per cm mouse movement

Defines the rotational increments (in degrees) for each centimeter of horizontal or vertical mouse movement along the x-, y- and z-axis in the input fields X, Y and Z.

Shifting in cm per cm mouse movement

Defines the horizontal and vertical increments (in centimeters) of shifting for each centimeter of horizontal or vertical mouse movement in the input fields Horizontally and Vertically.

Enlargement factor per cm mouse

Defines what value is to be added to the current enlargement factor, if the mouse is moved vertically for one centimeter. Horizontal increments are not taken into account.

Viewing distance per cm mouse

Defines what value is to be added to the current viewing distance, if the mouse is moved vertically for one centimeter. Horizontal increments are not taken into account.

Hide mouse cursor while tracking

If this checkbox is checked, the mouse cursor becomes invisible while you are in tracking mode. Thus the cursor cannot reach the window's borders so that you may rotate, shift and enlarge the structure nearly continuously. If this setting is switched off, the mouse cursor changes to a special symbol while you are in tracking mode and follows all mouse movements.

See also:

Rotating and Shifting the Structure

Changing Enlargement Factor or Viewing Distance With Mouse or Cursor


Stepping page (Options dialog)
Stepping

The Stepping page is part of the Options dialog. The settings on this page define the increments for the keyboard-controlled rotation, shifting of structures as well as variation of enlargement factor and viewing distance.

Degrees along ...axes per keystroke

Defines the amount or rotation (in degrees) along the x-, y- and z-axis for each single hit on a cursor or PageUp/PageDown key in the input fields X, Y and Z.

Shifting in cm per keystroke

Defines the amount of horizontal and vertical shift for each hit on a cursor key (numerous pad) in the input fields Horizontal and Vertical.

Enlargement factor per keystroke

Defines what value is to be added to the current enlargement factor for each hit on the Home or End key.

Viewing distance per keystroke

Defines what value is to be added to the current viewing distance for each hit on the Ins or Del key.

See also:

Rotating and Shifting the Structure

Changing Enlargement Factor or Viewing Distance With Mouse or Cursor


Load command (File menu)

Opens the Load dialog with a list of all compounds of the current structure file. This command is not available, if the current structure file contains only one compound.

See also:

Multiple Structure Descriptions in One File


Load dialog
Load

Offers a list of all compounds of a structure file. It is used to load one or more compounds from the structure file.

File...

Displays the path of the structure file and the number of compounds.

Settings

Opens the Structure list format dialog where you can define which data of each compound shall be displayed in the structure list.

Copy

Copies the selected lines from the structure list to the clipboard.

Print

Prints all or only the selected lines from the structure list.

See also:

Multiple Structure Descriptions in One File


Structure list format dialog
Structure list format

Defines which data are to be displayed in the Load dialog as well as the sort criterion.

Not selected items

Contains all data items, which have not been selected to be displayed in the list of the Load dialog, in alphabetical order. This list works with extended selection.

Selected items

Contains all data items, which have been selected to be displayed in the list of the Load dialog in the current order. Items in the list can be move up or down to change the order of the data items to be displayed in the list of the Load dialog. To move an item, move the mouse cursor to the item, press down the left mouse button, move the cursor to the desired position, and release the left mouse button at the final position.

>>

Moves the item(s) that is/are selected in the list Non selected items into the list Selected items. New items will be appended at the end of the destination list.

<<

Moves the item that is selected in the list Selected items back into the list Non selected items.

Sort for

Selects what the list in the Load dialog is to be sorted for. If [No sorting] is selected, the list will not be sorted.

Full Row Selection

If this checkbox is checked, the full row which contains the data for a compound in the Load dialog, will be marked, if the compound is selected. Otherwise only the first column will be marked.

Display Grid

If this checkbox is checked, a grid is displayed separating the rows and columns in the list of the Load dialog.

Remarks

For full row selection and grid, COMCTL32 Version 4.71 must be installed on your computer.

See also:

Multiple Structure Descriptions in One File


Save all command (File menu)

Saves the structure documents in all open structure windows with the existing names. If a structure has not yet a file name assigned, you will be prompted to enter a file name in the Save As dialog.

See also:

Saving Structural Data


Search command (File menu)

Opens the Search files dialog for the search of specified structural data in selected files.

See also:

Searching Structure Files


Search files dialog
Search files

Searches selected data files for specified structural data.

Path

Defines the path of searched files. See additional remarks below.

Browse

Opens the Browse dialog, which is similar to the standard Windows File Open dialog, to select file type and directory where the search is to be started.

Include sub-directories

If this checkbox is checked, Diamond searches all sub-directories of the directories defined in the path, too. See additional remarks below.

Foreign formats, too

If this checkbox is checked, Diamond also searches files in foreign (i.e. non-DSF) format. Otherwise only files in DSF are searched. See additional remarks below.

What to search for

Opens the What to search for dialog to specify the structural data (e.g. authors' names, chemical composition etc.) to be searched for.

Start search

Starts the searching procedure.

Result...

This list contains the complete paths of all matching structure files. This list works with extended selection.

Open

Opens the file(s) listed in the list of matching files.

Remarks

The search path defined in Path as well as the setting Include sub-directories define what files will be searched. The setting Foreign formats, too defines the formats of the files to be searched. If neither Include sub-directories nor Foreign formats, too are active, Diamond only searches files in DSF 2 format that match one of the names defined in the search path. The names in the path can have the "wild cards" * and/or ?. Additionally disk drive letter and directory should precede. Example: "C:\DIAMOND\ICSDDATA\AL*.DSF" searches all files in the directory "\DIAMOND\ICSDDATA" of drive C: beginning with "AL" and having the extension "DSF".

The setting Include sub-directories enables you to search entire directories trees - even complete disk drives. Example: "C:\*.DSF" searches all DSF files of drive C:.

If the setting Foreign formats, too is active, not only files in DSF 2 format are searched but also files in foreign (i.e. non-DSF) formats - as far as they are defined in the search path. The same file formats as in the file open procedure of Diamond are supported: CIF, SHELX, CSD-FDAT, PDB, Crystin, and XYZ. Foreign formats are recognized automatically.

After the search process has been started, it can be stopped with the Stop search button. Since the search process works with its own thread, you may continue working with Diamond, while the search process is running.

Since the list of matching files is list with extended selection, multiple files can be opened at the same time.

When closing the dialog all settings (especially search path and search criteria) are saved and are available during later sessions of Diamond, but not the contents of the matching list.

See also:

Searching Structure Files


What to search for dialog
What to search for

Defines what structural data files are to be searched for.

1. Section for text search

Text

If this checkbox is checked, Diamond searches for a text or a text fragment. Otherwise all settings of this section will be ignored.

as word

If this checkbox is checked, a text fragment found is registered as match only, if it represents a whole word, but not if it is only part of a longer word. That means neither the last character before nor the first character after the matching fragment must be a letter.

case-sensitive

If this checkbox is checked, the comparison is case-sensitive, i.e. "Structure" and "structure" are treated as different.

Search where

Switch the text categories (e.g. authors' names, title) on where you want to search the text fragment. Multiple categories may be selected at the same time.

Text (fragment)

Defines the text or the text fragment, rsp., to be searched for.

2. Section for search for chemical composition

Chemical composition

If this checkbox is checked, Diamond searches for a special chemical composition. Otherwise all settings of this section will be ignored.

Element(s)

Enter the symbol(s) of the element(s) to be included in the searched compounds (not mandatory). Multiple symbols are separated by blanks or commas.

OR connection

If this checkbox is checked, all compounds with at least one of the specified elements included match, else only those compounds match that contain all of the elements defined in Elements.

Formula type

Enter a formula type to select compounds with special stoichiometric composition (not mandatory).

Element count

Defines the number of different chemical elements that a matching compound must have (not mandatory). A single value can be specified as well as a range of numbers (the lower number in the left, the higher in the right input field).

Remark for the search for chemical composition

If the search for chemical composition is switched on (check button Chemical composition), at least one element or a formula type or a value for the number of the elements must be specified! Multiple definitions are connected logically AND.

3. Section for search for space groups

Space group

If this checkbox is checked, Diamond searches for (a) special space group(s). Otherwise all settings of this section will be ignored.

Number acc. to International Tables

If this radio button is checked, all compounds match with a space group number in the specified range of space group numbers. Even a single space group number can be specified, too.

Hermann-Mauguin symbol

If this checkbox is checked, all compounds match, which have the same Hermann-Mauguin space group symbol as defined in the opposite input field.

4. Section for search for Cell volumes

Cell volume

If this checkbox is checked, Diamond searches for compounds with a cell volume within the range defined in the opposite input fields. Otherwise the volume values are ignored.

5. Section for search for codes

Code(s)

If this checkbox is checked, Diamond searches for special codes (e.g. ICSD Collection Code, CSD Reference Code). Enter the code or multiple codes (separated by blanks) you want to search for in the opposite input field.

6. Section for search for date

Date

If this checkbox is checked, Diamond searches for structural descriptions created or last updated within a range of time. Enter the earliest and latest date of the desired range in the opposite input fields. For both earliest and latest date you may define a specific date in the format "dd-mm-yy" (day, month, year) or simply a single number for a year. You may also specify a single date or a single year instead of a range. If the setting Recording date is selected in the opposite combobox, the date of creation of a searched data set is taken into consideration. Otherwise (Update) the last update is taken.

Remarks

At least one of the six mentioned sections must be activated for the search. If multiple sections are active, the subsidiary results are connected logically AND.

When closing the dialog all settings and entered texts and numbers are saved and are available in later sessions of Diamond - even if you use this dialog e.g. for the search of files and then for the search in a thereafter opened list. This makes it easy to search for a special compound if you do not know the file where it is stored.

See also:

Searching Structure Files


Properties command (File menu)

Opens the Properties dialog which displays the data status (e.g. number of created atoms, polyhedra, etc.) of the current structure.


Contents page (Properties dialog)
Contents

The Contents page is part of the Properties dialog.

Contents

Displays the contents of several data fields and lists for the current structure.

Atomic parameters	the number of atoms in the parameter list
Symmetry records	the number of symmetry matrices (without Bravais translations) of the current space group
Atoms in unit cell	the number of atoms in the unit cell. This is the sum of the multiplicities of all atoms from the parameter list with valid coordinates
Explicitely defined bonds	the number of bonds which have been defined in the input file
Created atoms	the number of created atoms
Created bonds	the number of created bonds
Cell corners	the number of pseudo-atoms representing cell corners
Cell edges	the number of pseudo-bonds representing cell edges
Atom labels	the number of atom labels
Bond labels	the number of bond labels
Texts	the number of user-defined texts
Polyhedra	the number of coordination polyhedra
Polyhedron faces	the total number of polyhedron faces
Distances	the number of reported or measured distances
Angles	the number of reported or measured angles
Torsion angles	the number of reported or measured torsion angles


Created Atoms page (Properties dialog)
Created atoms

The Created Atoms page is part of the Properties dialog.

Number of created atoms...

This list displays the list of atom types of the current structure and how many created atoms of the current structure picture belong to these atom types.


Settings command (Data sheet context menu)

Opens the Data sheet settings dialog where you can select the data categories to be displayed or hidden in the data sheet.

See also:

Data Sheet: Contents


Data sheet settings dialog
Data sheet settings

Selects the data categories to be displayed or hidden in the data sheet.

Bibliographic data

If this checkbox is checked, bibliographic data will be displayed, such as the authors' names, title, but not crystal data, such as measured or calculated density, etc.

Crystal data

If this checkbox is checked, crystal data will be displayed, including space group and cell parameters.

Atomic parameters

If this checkbox is checked, atomic parameters will be displayed, including isotropic or equivalent anisotropic displacement parameters, but not the anisotropic displacement parameters.

Wyckoff symbol/Multiplicity

If this checkbox (and the Atomic parameters checkbox) is checked, a column with the Wyckoff symbol (letter) and the multiplicity of each site of the parameter list will be displayed.

Site symmetry symbol

If this checkbox (and the Atomic parameters checkbox) is checked, a column with the site symmetry symbol of each site of the parameter list will be displayed.

Anisotropic displacement parameters

If this checkbox is checked, anisotropic displacement parameters will be displayed.

Selected geometric parameters

If this checkbox is checked, measured or reported distances, angles, and torsion angles will be displayed.

See also:

Data Sheet: Contents


Save data/list as... command (Context menu)

Opens the standard MS Windows Save File As dialog, where you can define a text file to save the contents of the data sheet or list.

If this command is called from the data sheet, the contents of the data sheet can be saved as plain text or as Rich Text.

If this command is called from an object list or from the list of distances and angles, the contents can be saved as:

Text with separators	*.CSV	The contents of the columns of one row are separated by semicolons. Rows are separated by line feeds.
Text with tabs	*.TXT	The contents of the columns of one row are separated by tabs. Rows are separated by line feeds.
Formatted text with spaces	*.PRN	Each column has a fixed number of characters (filled with blanks if necessary). Rows are separated by line feeds.

See also:

Copying and Printing Data from the Data Sheet


Print command (File menu)

Prints the current structure picture, if the main pane is focussed, or the contents of the data sheet, object list, or list of distances and angles, rsp.

If this command is called from the File menu or via the accelerator Ctrl+P, the standard MS Windows Print dialog is opened, where you may change printer settings before printing.

If this command is called from the Standard toolbar using the [image] button, the structure picture, data sheet, or list will be printed directly using the default printer settings and without opening the Print dialog.

See also:

Printing, Copying, and Saving the Structure Picture: Overview


Update command (context menu)

Updates the contents of the data sheet or list of objects or list of distances or angles, rsp.


Select atom(s) command (Context menu)

Selects all created atoms which have been generated from the atoms that are currently selected in the atomic parameter list.

See also:

Selecting Atoms, Bonds, or Polyhedra From an Object List


Delete atom(s) command (Context menu)

Deletes the selected atom(s) from the parameter list. Deletes all symmetry-related atoms from the structure picture that have been derived from the corresponding atoms of the parameter list.

See also:

Editing atomic parameters


List format command (Context menu)

Opens the List format dialog, where you can define the items to be displayed for each object (atom, bond etc.).

See also:

Object Lists: Contents and Settings


List format

Defines which data are to be displayed for each object of the current list (atom list, bond list, etc.).

List...

Contains all data types which can be displayed in the object list. Those data types will be displayed with a check mark set.

Sort for

Selects the data type which the object list is to be sorted for, or "[No sorting]", if the items shall not be sorted.

Descending

If this checkbox is checked, the items in the object list are sorted for the criterion in Sort for in descending order, else in ascending order.

Full Row Selection

If this checkbox is checked, the full row which contains the data for a compound in the Load dialog, will be marked, if the compound is selected. Otherwise only the first column will be marked.

Display Grid

If this checkbox is checked, a grid is displayed separating the rows and columns in the list of the Load dialog.

Enable Header Drag&Drop

If this checkbox is checked, columns can be shifted (that means rearranged) by dragging with the mouse to the desired position.

Remarks

For full row selection, grid, and header drag&drop, COMCTL32 Version 4.71 must be installed on your computer.

See also:

Object Lists: Contents and Settings


Add command (Context menu)

If the list displays distances only, the selected distances will be added to the list of reported or measured distances.

If the list displays angles or both distances and angles, the selected angles will be added to the list of reported or measured angles.

See also:

Adding Selected Distances or Angles to Geometric Parameters


Settings command (Context menu)

Opens the Settings for distances and angles dialog, where you can define if distances and/or angles are to be displayed, as well as the distance and angle range and the atom types to be concerned.

See also:

List of Distances and Angles


Settings for distances and angles dialog
Settings for distances and angles

Defines if distances and/or angles are to be displayed, as well as the distance and angle range and the atom types to be concerned.

Display

Defines if distances or angles are to be calculated and displayed or both.

Distances' range

Defines lower and upper bound for distance calculation, in Angstroems.

Angles' range

Defines lower and upper bound for angle calculation, in Angstroems.

Calculate distances (and angles) between...

Both lists contain all atom types of the current compound. All atoms of the parameter list whose associated atom types are selected in the left list, will be taken as central atoms of the distance spheres. Diamond will calculate distances to all atoms belonging to the atom types selected in the right list.

Apply

Applies the settings to the list of distances and/or angles without closing the dialog.

See also:

List of Distances and Angles


Standard uncertainties command (Context menu)

If this menu item is checked, standard uncertainties will be calculated and displayed for the distance and angle values.

See also:

List of Distances and Angles


Coordination number command (Context menu)

If this checkbox is checked, identical distances between the same central atom and the same (but symmetry-equivalent) neighbour will be collected, and the number of these identical distances displayed.

See also:

List of Distances and Angles


Repeat first symbol command (Context menu)

If this checkbox is checked, the symbol of the central atom will be displayed in every row. Otherwise the symbol of the central atom will be displayed only for the first distance with this central atom.

See also:

List of Distances and Angles


Unit | Angstroems command (Context menu)

If this menu item is checked, distances will be displayed in Angstroems.

See also:

List of Distances and Angles


Unit | Picometers command (Context menu)

If this menu item is checked, distances are displayed in picometers.

See also:

List of Distances and Angles


Unit | Nanometers command (Context menu)

If this menu item is checked, distances will be displayed in nanometers.

See also:

List of Distances and Angles


Symmetry code | No code command (Context menu)

If this menu item is checked, no symmetry information will be displayed for the second atom, if distances are displayed, as well as for the two atoms at the sides, if angles are displayed.

See also:

List of Distances and Angles


Symmetry code | Symmetry matrix command (Context menu)

If this menu item is checked, symmetry information will be displayed for the second atom in the format "x,y,z", if distances are displayed, as well as for the two atoms at the sides, if angles are displayed.

See also:

List of Distances and Angles


Symmetry code | Atom code command (Context menu)

If this menu item is checked, symmetry information will be displayed for the second atom as atom code, if distances are displayed, as well as for the two atoms at the sides, if angles are displayed.

See also:

List of Distances and Angles


End tracking mode command (Tracking toolbar)

Ends the tracking mode. The mouse cursor will return to its standard arrow symbol.

See also:

Rotating and Shifting the Structure


Rotation X/Y command (Tracking toolbar)

Switches to tracking mode with rotation along x- and y-axis of the view coordinate system, while the left mouse button is pressed.

See also:

Rotating and Shifting the Structure


Rotation Z command (Tracking toolbar)

Switches to tracking mode with rotation along the z-axis of the view coordinate system, while the left mouse button is pressed.

See also:

Rotating and Shifting the Structure


Shift command (Tracking toolbar)

Switches to the tracking mode where the structure's position follows horizontal and vertical shifts of the mouse simultaneously, while the left mouse button is pressed.

See also:

Rotating and Shifting the Structure


Enlargement factor command (Tracking toolbar)

Switches to the tracking mode where the enlargement factor follows vertical shifts of the mouse simultaneously. Moving down the mouse (with left mouse button pressed) enlarges, moving up reduces the structure.

See also:

Changing Enlargement Factor or Viewing Distance With Mouse or Cursor


Viewing distance command (Tracking toolbar)

Switches to the tracking mode where the viewing distance follows vertical shifts of the mouse simultaneously. Moving down the mouse (with left mouse button pressed) reduces, moving up enlarges the distance.

See also:

Changing Enlargement Factor or Viewing Distance With Mouse or Cursor


Limitations of the Demonstration Version

This article informs you about limitations of the demonstration version as compared with the full version of Diamond. This information is not valid for the full version of Diamond.

The demonstration version is identical with the full version except of the restrictions mentioned below:

No saving

Changes in structure documents cannot be saved in the original file format of Diamond (the Diamond Structure File format, DSF) - for the file version 2 as well as for the older file version that was used by the version 1.x of Diamond.

That means, whenever you call one of the functions that save the current structure document either with the "old" file name (File / Save) or with a new file name (File / Save as...), this will fail. Instead, a message box will remember you of this restriction.

Additionately, the function "File / Save all" is not available for this reason.

If you close a structure window - either by closing the window, by using the "Close all" command from the "Window" menu, or by closing the application window of Diamond -, this will be closed immediately, even if the structure document has been changed or is new. That means, the usual prompt ("Save modifications in...?" - Yes/No/Cancel) will not appear!

The "Auto Save" function - which you can find on the Desktop tab of the Options dialog (Tools / Options) will not work, too.

"Diamond Demonstration Version" banner

A banner with "Diamond Demonstration Version" will be written into saved bitmaps, Windows Metafiles, and printouts.


Ordering Informations for the Full Version of Diamond

Using Internet Order Form

The most suitable way to order the full version of Diamond is to make use of the Diamond Web pages on the Internet - supposed you are connected to the Internet and have a World-Wide Web browser (e.g. Microsoft Internet Explorer or Netscape Navigator).

Open the Diamond Order Page which has the address

http://www.crystalimpact.com/diamond/order.htm

Fill out the order form completely, and press the "Submit" button once. This will generate an email that will be sent to us, which contains the informations that you have given in the order form.

Downloading, printing out, and filling out of the Order Form

Another way is to print out the order form, which is available as MS Word document, and can directly be opened from the Diamond Order Page (http://www.crystalimpact.com/diamond/order.htm). (This requires MS Word installed on your computer.) Send the filled out order form as fax to:

++49 - 2 28 - 73 95 86

Or mail it to:

Crystal Impact GbR

Postfach 1251

D-53002 Bonn, Germany

Requesting Order Form by email or fax

Another way is to request an order form, which we can send to you either by mail, as fax, or attached to an email. To request the order form, send an email to:

sales@crystalimpact.com

Or fax it to the fax number given above, or mail it to the address given above.


Tracking mode

Special mode where the structure follows the mouse movements simultaneously. This can be a rotation along x- and y-axis, a rotation along z-axis, a shift within the drawing area, enlargement or reducing, or a variation of the viewing distance (camera distance).


Stepping

Rotation of the structure, shift within the drawing area, enlarging or reducing, or a variation of the viewing (camera) distance step by step using specific keys.


Formula type

Represents the stoichiometry of the compound. Elements with positive oxidation numbers are indicated with the first letters of the alphabet (A-M), elements with negative oxidation numbers with the last letters (X-Z, W, V, U, T, S), and elements with oxidation number 0 with the letters N-R. Hydrogen and its isotopes are not considered unless they have the oxidation number -1. If an element occurs in different oxidation numbers in the same compound, different letters must be used. Letters are sorted for ascending indices within one and the same group of letters.

For a defect structure incomplete site occupation is not taken into consideration. But atoms on the same site (i.e. mixed sites) are considered as equal and indicated with the letter of the most common element.

Examples:

Ca2SiO4	AB2X4

CaSO4 (H2O)2	ABX6	(sulphate's O and water's O are summarized)

(Na0.2K0.8)(AlSi3)O8	AB4X8	(mixed site of Na and K)

NaTl	NO	(intermetallic compound, oxidation numbers 0)

H2O	X	(positive hydrogen is not considered)

CaH2	AX2	(hydrid anions)

Na2S2O3	AB2XY3	(S in two different oxidation numbers)


Session

A Diamond session begins with the start of the program and ends with the closing of the application.


Relative Entry Number

Indicates the serial number of a crystal structure description within a file, beginning with 1. Since the structure list may be sorted, the rank order in the list does not necessarily agree with the order in the file.


Formula sum

Represents the stoichiometric composition which has been calculated from the parameter list. Therefore site occupation factors and multiplicities of the atomic parameters are used as well as the number of formula units in the unit cell.


Structural formula

Element symbol and stoichiometric indices are arranged to express components (e.g. molecule ions). This formula need not agree with the formula sum generated from the parameter list.


Analytical formula

Represents elements and stoichiometric indices resulting from a separate analytical determination and often contains trace elements which do not appear explicitely in the parameter list. Thus the formula need not agree with the formula generated from the parameter list.


Wyckoff sequence

Determines what sites are occupied by how many atoms. The sequence consists of letters and integer numbers. The letters represent the Wyckoff symbols of the sites, the indices the number of asymmetric atoms on each site. The letters are noted in reverse alphabetic order.

Examples: a7 means that only the a site is occupied (by seven asymmetric atoms); f b2 a represents one asymmetric atoms on sites f and a each and additionally two atoms on site b.


Pearson symbol (Pearson code)

Defines centering, crystal system, and the sum of the multiplicities of all sites in the atomic parameter list. The first character is a lower case letter defining the crystal system (with a for anorthic = triclinic; trigonal is given as hexagonal). The second character is an upper case letter defining the centering. The multiplicity is given immediately after these two letters.


Authors

The authors’ names are given in Diamond: surname <blank> capital(s) of the prename(s). Names of multiple authors’ are separated by commas.


Title

Represents usually the title of the publication of the structure. But beyond that any title can be assigned by the user.


Citation

Represents the ASTM Journal Coden of the periodical as well as volume number, first and last page and the year.


Trivial name

Represents the usual (trivial) name of the compound, i.e. a name that need not agree with IUPAC nomenclature.


Systematic name

Represents the complete name according to IUPAC or Chemical Abstracts nomenclature, e.g. lithium[4,6,7,11-tetramethyl-3,5,8,10-octakis-(methylamino)-spiro[5,5]tetrasila-2,9-dioxa-4,6,7,11-tetraaza-1-aluminate].


Structure type

Represents the name of the structure type. Usually a structure type is applied to minerals and inorganic compounds only, e.g. perovskite, sphalerite, C3


Mineral name

Represents a mineral name defined by the International Mineralogical Association, e.g. chalcopyrite.


Source of compound or mineral

Describes the place where a mineral was found or the origin of a natural product, e.g. from Kaiserstuhl, Germany.


Comment

Enables the definition of a (maximum 32k long) multiline comment. If the compound has been imported from a crystallographic database, this field may contain data that do not fit the standard data fields of DIAMOND, e.g. PRE 5 GPa; TWI (from ICSD: measured at 5 GPa; twinned crystal).


ASTM Journal Coden

Five character code for a journal’s title. This can be succeeded by a sixth character (proof character), e.g. ANCEA.


Standard uncertainties (Standard deviations)

Standard uncertainties may be given in Diamond optionally for lattice constants and atomic parameters in brackets directly attached (without blanks) to the numerous value, e.g. 0.4386(22) means a standard uncertainty of 0.0022.


Coordinate systems

DIAMOND distinguishs between three coordinate system:

The crystal coordinate system describes a coordinate system defined by the three basic vectors of the unit cell a, b and c. Thus crystal coordinates (x/a, y/b and z/c) have no dimensions. The corner opposite of the origin (0,0,0) has the coordinates (1,1,1) in any case.

The reference coordinate system describes a rectangular (right-handed) coordinate system with unit length 1 Angstroem. Thus coordinates x, y and z are given in Angstroem in any case. The x-axis runs parallel with the a-axis of the crystal coordinate system, y lies in the ab-plane (and is parallel with b if the angle  has 90°), and z points to the viewer.

The view coordinate system is rectangular and right-handed like the reference coordinate system. But the axes x, y and z are fixed independent of the current orientation of the structure. Thus the x-axis points to the right, the y-axis to top and the z-axis to the viewer.


Colors

You may select predefined colors in special comboboxes (e.g. Red, Dark grey etc.). The color Auto is normally identical with white unless the structure picture is represented in the black-on-white mode, i.e. on white background. In this case Auto means black.

In certain cases the color may be composed by the user. Therefore select the ‘color’ Customized and push the opposite button Color.


Model

Usually a crystal structure will be represented in the ball-and-stick model with atoms as spheres (or ellipsoids) and bonds as thin lines or tubes. Only this standard model enables the representation of coordination polyhedra and thermal ellipsoids.

The wire model displays only the bonds as thin lines with the colors of the bonded atoms in parts. Non-bonded atoms are displayed as dots.

The space-filling model displays only atoms (and cell edges) but no bonds. The radii of the spheres representing atoms are taken from the van der Waals radii.


Connectivity

Describes a list of all N(N+1)/2 combinations of N atom types of a structure. For each atom type pair a bonding sphere is defined and a flag if this bonding sphere is active or not, i.e. whether bonds are allowed for that atom type pair or not.


Generic sphere

Defines a sphere around a central atom that is searched for bonded atoms (ligand atoms). The size of the sphere (inner and outer bound) depends on the types of central and ligand atom and is defined in the connectivity. Bonds between central and ligand atom will automatically be created.


Fixed sphere

Defines a sphere around a central atom that is searched for neighbouring atoms. The inner and outer bound are independent of the types of central and ligand atoms. No bonds between central and ligand atoms will be created automatically.


Toolbar

This toolbar is available only if a structure picture is active (‘focussed’). It is placed between the main window and statusbar and contains several symbols representing commands for building up a structure.


List with extended selection

Enables the independent selection of multiple entries of a list. You may mark successive entries by moving the mouse cursor with left mouse button down vertically through the list. Or use the keys Cursor up or Cursor down with the Shift key pressed down. If you press the Ctrl key and click an entry with the mouse, this entry will be marked on or off independent of the other entries.


List with multiple selection

Enables the independent selection of multiple entries of a list. If you click an entry with the mouse, this entry will be marked on or off independent from the other entries. You can also use the Cursor key to move to the desired position and select the item with the Spacebar or clear the selection, rsp.


Atom code

Defines how to create an atom from a specific atom of the parameter list by applying specific symmetry operators, Bravais translations and integer cell translations. The code has the general form AXYZSSB and is similar to the code used in the program ORTEP. A is the number of the atom in the parameter list (the first atom has number 1). SS is the number of the symmetry operation and B the number of the Bravais translation. Both SS and B depend on the space group and can have a maximum of 48 and 4 rsp. X, Y, and Z determine what integer values (minus 5) must be added to the x-, y- and z-coordinates (crystal coordinates). That means no integer cell translations will be applied if XYZ is "555". For "364" e.g. -2 is added to the x-, +1 to the y- and -1 to the z-value.


Formula weight

Diamond distinguishes between two kinds of formula weights:

(1) The formula mass in daltons measured by a non-diffraction experiment. This corresponds to the CIF data name _chemical_formula_weight_meas.

(2) The formula mass calculated by Diamond from the atomic parameter list. This is the sum of the atomic masses of the chemical elements defined in the atomic parameter list regarding multiplicities and site occupation factors, and then divided by the number of formula units (Z). This corresponds to the CIF data name _chemical_formula_weight.


Number of formula units in the unit cell (Z value)

An integer value used to calculate the formula sum from the elements in the atomic parameter list.

Example:

The unit cell of sodium chloride (standard modification) contains 4 Na and 4 Cl atoms. The Z value of 4 is used to get the stoichometric indices of 1 in NaCl (Na4 Cl4 / 4 = NaCl).


Density

Diamond distinguishes between two kinds of densities. Both densities are given in grams per cubic centimeter.

(1) The measured density using standard chemical and physical methods. This value corresponds to the CIF data name _exptl_crystal_density_meas.

(2) The density calculated from the calculated formula weight, the number of formula units (Z) and the cell volume (cvol):

density_calc = fweight_calc * Z / cvol * 1.0 / 0.60225


Residual factor ("R value")

Diamond stores the residual factor for all reflection data as well as the factor for those reflection data classified as "observed". These factors correspond to the CIF data names _refine_ls_R_factor_all and _refine_ls_R_factor_obs rsp. R = Fm - Fc / Fm, where Fm and Fc are measured and calculated structure factors. This is the conventional R factor.


Clipboard

The MS Windows clipboard is used to exchange data of several formats (text, bitmap graphics, etc.) between applications. In Diamond you can e.g. copy parts of a list or data sheet as text to the clipboard. This text can be pasted by other applications, e.g. word processors.


Rich-Text Format (RTF)

The rich-text format (RTF) standard is a method of encoding formatted text and graphics for easy transfer between different programs and different operations. Generally, it is used by Microsoft Word and many other word processors for moving word-processing documents between different platforms without having to rely on special translation software or conversion utilities. Diamond uses this format to copy the contents of the data sheet to the Windows clipboard or to save it directly to a file.


Panes

The Diamond structure window consists of two different parts, called "panes", the main pane, which displays the structure picture, and a secondary pane on the right that displays textual information such as the data sheet, the list of distances and angles, or several lists for objects (atoms, bonds, etc.). The main pane is often called "graphics pane", the secondary pane often "data pane".


Data sheet

The data sheet displays textual information about the current structure and can be displayed in the secondary pane (or "data pane") of the structure window. The output is formatted (tabs, bold, superscripts, etc.) and can be copied in that way to word processors or printed directly.


CIF symmetry code

A code consisting of a single number or of the type "S_XYZ". The single number or the number "S" is the sequence number of the symmetry elements as listed in the _symmetry_equiv_pos_as_xyz loop. "XYZ" are connected integer cell translations along the a, b, and c axes with respect to the base number "555".
Examples:

".": no symmetry operations or translations;

"4": 4th symmetry operation to be applied;

"7_645": 7th symmetry operation, +1 in a-, -1 in b-direction, no translation in c-direction.


Dummy atom

A dummy atom is an atom in the parameter list or its symmetry equivalent created atom, which has coordinates but no chemical meaning. It is normally used as a geometric auxiliary point, for example in the center of a cyclopentadienyl ring or the center of a polyhedron.


Auto color

This color is white in normal mode (where the background color is usually rather dark). In black-on-white mode it is black, instead.


Black-on-white mode

In black-on-white mode, the background is painted or remains white. The background color will be ignored. The color "Auto" is black.


Color select box

A special kind of combobox where you can select from pre-defined colors, including the Auto color, store user-defined colors as well can request a new color. To define a new color, scroll down to the bottom of the color select box, which will automatically open the MS Windows standard dialog to define a new color or select a color from existing colors.


About Diamond Online Help

The Diamond Help Library gives you unified access to the Diamond online help. The library consists of the following parts:

(1) An introduction to Diamond

(2) An overview for experienced users of Diamond 1.x what is new in version 2.0.

(3) An online user manual.

(4) A tutorial which will make you familiar with the wide variety of functions in Diamond.

(5) A list of hints and tips.

Additionally, the Help Library contains context-sensitive help for commands, toolbar buttons, and dialog boxes. This help is available with the F1 key.

For the latest versions of Diamond help files, visit the Diamond support page on the Web (http://www.crystalimpact.com/diamond/support.htm). The Diamond page will also offer answers to many commonly asked questions and new information about Diamond that may not appear in the documentation.

---  Diamond Help Library  ---  Last modified: 21 December 1998


Hardware and Software Requirements

To install and run Diamond Version 2.0, you should have the following

system requirements:

(a) Minimum system requirements

Microsoft Windows 95 or 98 or Windows NT 4.0 operating system

Personal Computer with Intel i486 (or compatible processor)

16 megabytes of RAM (Windows NT: 32 megabytes)

70 megabytes of free disk space (100 megabytes during installation)

Graphics resolution of 800 x 600 pixels with 256 colors

CD-ROM drive

Microsoft-compatible mouse

(b) Optimum system requirements

Microsoft Windows 95 or 98 or Windows NT 4.0 operating system

Personal Computer with Intel Pentium (or compatible processor)

32 megabytes of RAM (Windows NT: 64 megabytes)

70 megabytes of free disk space (100 megabytes during installation)

Graphics resolution of 1024 x 768 pixels or higher with

    32,768 or more colors ("High Color", "True Color")

CD-ROM drive

Microsoft-compatible mouse


Software Licence Agreement

End-User License Agreement for

DIAMOND Visual Crystal Structure Information System

between you and

CRYSTAL IMPACT

- Important information! Please read carefully -

The software product mentioned above (the ”Software Product”) includes media in electronic as well as printed form (installation diskettes, online help, and user manual).

Before proceeding with the installation and/or use of this software, read the following terms and conditions of this license agreement and limited warranty carefully (the ”Agreement”).

By installing or using this software you indicate your acceptance of this agreement. If you do not accept or agree with these terms, you should not install or use this software.

1. Grant of license

This Software Product is owned by CRYSTAL IMPACT Dr. K. Brandenburg & Dr. M. Berndt GbR ("CRYSTAL IMPACT") or by its suppliers and is protected by copyright law and international treaty provisions. This agreement does not provide you with title or ownership of the Software Product, but only a right of limited use. If you have acquired one or more special licenses ”for use in academic institutions only”, you are restricted to use these licenses at schools, universities, or other non-commercial researching and educational institutions, exclusively.

2. Restrictions

a) Number of users: The number of installations at a time is limited to the number of licenses you have purchased.

b) Reverse engineering: You are not permitted to disassemble or reverse compile the Software Product for the purpose of reverse engineering.

c) Copying: You are not permitted to forward copies of the Software Product to any third person. Copies of the Software Product may be made for personal archival or backup purposes, only.

d) Rental or leasing: You are not permitted to rent or lease the Software Product.

e) Alienation: You are permitted to alienate the Software Product, only in whole but not in part, provided that you have destroyed all backup copies of the Software Product, and the new user will conclude a license agreement with CRYSTAL IMPACT without additional royalty.

3. Publications

You are permitted to publish data, produced with the Software Product, without restrictions and without additional royalties, provided that the publication contains the following citation:

DIAMOND - Visual Crystal Structure Information System

CRYSTAL IMPACT, Postfach 1251, D-53002 Bonn

4. Copyright

All title and copyrights in and to the Software Product, the accompanying printed materials, and any copies of the Software Product, are owned by CRYSTAL IMPACT or its suppliers. The Software Product is protected by copyright laws and international treaty provisions. Therefore, you must treat the Software Product like any other copyrighted material except that you may either (a) make one copy of the Software Product solely for backup or archival purposes, or (b) install the Software Product on a single computer provided you keep the original solely for backup or archival purposes.

5. Limited warranty

This Software Product is provided ”AS IS” without warranty of any kind either expressed or implied, including but not limited to the implied warranties merchantibility and fitness for a particular purpose. The entire risk as to the quality and performance of the Software Product is with you. Should the Software Product prove defective, you assume the cost of all necessary servicing or error correction.

CRYSTAL IMPACT does not warrant that the functions contained in the Software Product will meet your requirements or that the operation of the software will be uninterrupted or error free.

6. Limitation of remedies and liability

In no event shall CRYSTAL IMPACT, or any other party who may have distributed the Software Product as permitted above, be liable for damages, including any general, special, incidental, or consequential damages, arising out of the use or inability to use the Software Product (including, but not limited to, loss of data or data being rendered inaccurate or losses sustained by you or third parties or failure of the Software Product to operate with any other products), even if such holder or other party has been advised of the possibility of such damages.

The cumulative liability of CRYSTAL IMPACT to you for all claims relating to the Software Product, in contract, tort, or otherwise, shall not exceed the total amount of license fees paid to CRYSTAL IMPACT for the relevant Software Product. The foregoing limitation of liability and exclusion of certain damages shall apply regardless of the success or effectiveness of other remedies.


Support

In case of trouble when using Diamond (and the Help Library and the Readme file should not help you), you can consult our Diamond Support Page:

http://www.crystalimpact.com/diamond/support.htm

Or send email to:

support@crystalimpact.com

Or - if your are not connected to the Internet - send a fax to:

++49 - 2 28 - 73 95 86

The Diamond Support Page offers the latest versions of online help files, sample files, and software patches of the executables and DLL's.

The Diamond Support Page will also offer answers to many commonly asked questions and new information about Diamond that may not appear in the documentation.


Functions

•	32 Bit MS Windows 95/98/NT 4.0 application with Multiple Document Interface (MDI), object-oriented menus, toolbars and local popup-menus. Allows 'simultaneous' handling of multiple structures.

Input and Output:

•	Proprietary binary Diamond Structure File format (DSF) for rapid data access, including chemical and crystallographic as well as bibliograhic data. Saves your own built-up and designed frameworks of crystal structures.

•	Number of atoms, bonds, polyhedra etc. limited only by RAM.

•	Manual input or update of chemical, crystallographic, and bibliographic data.

•	Search for chemical, crystallographic, or bibliographic data.

•	Automatic import from data formats:

•	CRYSTIN download format created by ICSD or CRYSTMET

•	Cambridge Structural Database FDAT format.

•	Brookhaven Protein Data Bank format.

•	SHELX-93 format.

•	Crystallographic Information File (CIF).

•	XYZ format (free format with cartesian coordinates).

•	Export to CIF, SCHAKAL, XYZ and VRML format.

•	Snapshot of structure picture as high resolution bitmap or Windows metafile for post-processing (e.g. in a word processor).

•	Printing of structure lists or of selected datasets or structure pictures. Textual copy of datasets via Windows clipboard for post-processing.

Construction:

•	Filling of unit cell, multiple cells, any cell range, or boxes or spheres around selected central atoms.

•	Filling of user-defined rectangular areas within the screen.

•	Selection of atoms to construct sublattices.

•	Discussion of connectivity assisted by histograms showing the distribution of distances between selected atom types, together with automatic calculation and checking of distance ranges.

•	Generation of atoms from parameter list serving as initial atoms for building up complex frameworks.

•	Completion of coordination spheres around selected atoms.

•	Automatic generation of molecules or completion of fragments which has been clipped at cell edges.

•	User-controlled dismantling of built-up frameworks.

•	Multiple-step Undo and Redo function to enable safe experimentation with even high-complicated and unknown structural frameworks.

Visualization:

•	Ball-and-stick, wire, and space filling model. Central or parallel projection, depth cueing, and stereo display.

•	Photorealistic rendered models with user-defined light source and material properties (OpenGL).

•	Variation of colors, styles and radii of atom types and bonds. Labelling of atoms and bonds. User-defined text. Individual design of each single atom is possible.

•	Generation of coordination polyhedra (optionally with transparent surfaces).

•	Display of thermal ellipsoids.

•	Alternative color differentation to visualize oxidation numbers, site occupation factors etc.

•	Rotating, shifting, and zooming of structures: numerically, mouse-controlled, or keyboard-controlled. Definition of views along special axes or toward special planes.

Exploration:

•	Calculation of distances and angles. Measuring of distances, angles, and torsion angles interactively (incl. standard deviations).


Introduction

Acting as a visual crystal structure information system, Diamond integrates a multitude of functions which overcome the daily work with crystal structure data, mainly their visualization. With its high data capacity, its wide range of functions beginning with the generation of molecules reaching up to the construction of rather complicated inorganic structural frameworks, Diamond is the tool for molecular and solid state chemists as well as for surface and material scientists.


Changes from Version 1.2 to 2.0

As a specialist for complex inorganic crystal structures, DIAMOND is a well-known research tool and teaching aid. With its improved functionalities the program is now also a perfect tool for publication and presentation of crystal structures.

Graphics capabilities

The most obvious improvements relate to the graphics output. DIAMOND now supports the OpenGL graphics library. Thus the display of photo-realistic shaded models with user-defined light sources, materials properties and optional transparency is possible. Of course the common old-style drawing mode, which is more useful for black-on-white printouts, is also supported.

Handling

Although the smart handling of data and pictures has been a strength of DIAMOND in the past, it has been improved significantly. The method of editing a structure is analogue to edit a text within a word processor, e.g. first select particular objects to be edited and then choose a function to be applied on the selected objects. Thus the problem of editing a complex structure is reduced to the problem of smart selection.

Besides the possibility to click on one or multiple atoms (bonds, polyhedra etc.), each structure window can be divided into a picture frame and a text frame. In the text frame lists of atoms, atom types, polyhedra and other object types can be displayed and sorted individually. Once the objects are displayed properly according to your selection criteria, some mouse clicks on the list selects the corresponding objects within the structure frame. Context-sensitive popup-menus and 'flying' toolbars guarantees short ways to frequently used functions.

Capacities

Since DIAMOND is now a native 32-Bit application, all former restrictions of the maximum number of atoms, bonds, polyhedra etc. have been dropped. The number of objects in your structure model is now only limited by yours computer RAM.

VRML Export

DIAMOND graphics can be published in the internet by export them in VRML format (Virtual Reality Modeling Language). Now other people can study your structure models interactively - without having DIAMOND - by using a conventional Web browser.


Changes from Version 2.0 to 2.1

The changes from version 2.0 to 2.1 consist of a lot of slight changes and enhancements. These changes have been become available through several patches of the original version 2.0.

This is a list of changes and enhancements. (You can find a list sorted for patches/dates in the Readme.txt file.)

Enhanced cell edge drawing

Diamond now uses an enhanced algorithm for the drawing of cell edges. This affects only ball-and-stick and space-filling model in the standard (not rendering) mode. This algorithm avoids wrong overlap of atoms and cell edges, especially when drawing packing diagrams in a clinographic projection. (Older versions drew every cell edge in one part, whereas the new algorithm uses as many segments as needed.) The enhanced algorithm also calculates cutting between cell edges and atoms on or nearby the cell edges or corners. If you want to switch off enhanced cell edge drawing, disable the checkbox "Enhance cell edge drawing" in the "Objects/Cell edges" dialog.

Insert bond mode

There is now a second way to insert bonds between two atoms each. The "Insert bond" command from the Structure menu starts a mode where you can connect two atoms each with a bond. In this mode, the cursor changes to a special symbol. Then click on the first, then on the second atom where the bond is to be inserted. The structure picture will be refreshed automatically by Diamond after the second atom has been clicked. Now you can continue with the second pair of atoms, etc. To end this mode, choose the "Insert bond" command again, or press the Escape key. (The cursor will change to its usual arrow symbol.) The previous method still works with the "Insert bond" icon in the Build toolbar.

New polyhedron build mode

There is now a second way to build a single polyhedron. If three or more atoms have been selected, Diamond asks you if you want to use these N selected atoms as N central atoms for N polyhedra or if you want to build a single polyhedron with these N atoms as coordinating atoms of the polyhedron. If you choose the second method, you will be prompted for the central atom of the polyhedron to be constructed. (Diamond proposes the atom closest to the center of the selected atoms.) You can also tell Diamond to create a Dummy atom as central atom.

View towards plane with hkl indexes

The "Display/View" dialog now differentiates between h,k,l and u,v,w values to specify a defined orientation. h,k,l are the Miller indexes describing a plane that is parallel with the xy plane of the view coordinate system, that means parallel with the screen or printout page, whereas u,v,w define the three components of a vector in crystal coordinates that is to be transformed to the z-axis of the view coordinate system, that means shall point towards the user. In previous versions the hkl values led to wrong results if they were different from 0, 1, or -1.

Rotatable bond labels

Bond labels may now rotate with the bond axis. The new attribute "parallel" has been added to the existing alignment attributes for labels (centered, left, right).

Histogram up to 10 Angstroems

In the Connectivity dialog (command "Structure/Connectivity..."), you can now check distances up to a maximum of 10 Angstroems. (The old limit was 5 Angstroems.)

Site Symmetry Symbol

The data sheet (Data pane) can now display the Site Symmetry Symbol of each atom of the  parameter list. Wyckoff symbol and Site Symmetry symbol can be hidden using the dialog "Settings for data sheet" ("Settings..." command from the context menu), which has been extended for that case.

The site symmetry symbol (e.g. "2.mm" for the site "2a" in space group P42cm; no. 101) is now available in the atomic parameter list in the secondary (text) pane as well as in the info window of the Symmetry dialog.

Others

In the list of created atoms as well as in the list of bonds between created atoms, the columns for coordinates have been splitted to three columns each, that means X, Y, and Z will now be treated independently from each other (important if you forward the list to a spreadsheet or word processor table).

A new page on the "File/Properties" dialog shows the distribution of created atoms on the different atom types of the current structure. This information substitutes the old "Current formula", which was used in Diamond version 1.x on the "Display/Data status" dialog.

You can now select which atom types are to be displayed in the legend ("Objects/Legend..."). This gives you the opportunity to suppress atom types although they are part of the structure picture. The checkbox "Hide atom types not used in structure picture" has been moved from the "Legend" dialog box to the "Select atom types for legend" dialog box.

Atoms can now be deleted directly from the atomic parameter list (Data pane) with the new command "Delete atom(s)" from the context menu of the atomic parameter list (Data pane).


Bugfixes from Version 2.0 to 2.1

This is a history of bugfixes from version 2.0 to the current version 2.1. It is sorted for the dates of the patch releases 2.0a, 2.0b, etc.

For bugfixes in versions higher than 2.1, see the Readme.txt file, which contains the latest informations.

Version 2.0a  -  Date of Release: 12 June 1998

- The '&' character did not appear in the Licensee field in the About Diamond

  dialog box.

- Wrong angles in the list of distances and angles which is displayed in the data pane.

- Wrong restrictions in the Cell parameters dialog, if the space group of the current

  compound was trigonal.

- Some symmetry matrices were coded wrong in the space group info file FINSGRN.DAT,

  for example "x,x+2,z" instead of "x,2x,z". This error affected some trigonal and

  hexagonal space groups.

- Automatic recognition of Wyckoff symbols and multiplicities did not work correct

  during file conversion and after editing of atomic parameters.

- Symmetry matrices such as "x,2x,z" were given as "x,x,z", for example in the

  Symmetry dialog.

- When creating atoms from the Add atoms dialog, the created atoms sometimes

  got wrong atom codes, containing illegal symmetry indexes. This led to errors

  or crashes when displaying these codes in the atom list in the data pane.

Version 2.0b  -  Date of Release: 25 June 1998

- "Create infinitesimal bonds" has been replaced by the correct term

  "Create broken-off bonds" in the Fill coordination spheres dialog.

- When calling the function "Add all atoms" from the Structure menu, all but

  the last atom from the parameter list were created.

- On some installations, Diamond crashed everytime you press the right mouse button

  to request a context menu. This crash did also appear when using Shift+F10 or

  the context menu key on a MS Windows 95 keyboard.

Version 2.0c  -  Date of Release: 3 August 1998

- When you pushed the "Connect" button in the Connectivity dialog (command "Structure/

  Connectivity..."), the current settings in the dialog were ignored. Instead, the

  settings valid when opening the dialog were used.

- In some cases, Diamond showed "-1.#IND0" instead of an angle value when displaying the

  (current) orientation.

- In the Load dialog, a dummy value was displayed for Journal coden, volume and pages

  instead of the correct values.

- In most network installations, Diamond had no access to the Key File, which contains

  serial number and name of the licensee, so that you had to edit the path to the Key File

  manually after installation on every Client computer that accessed Diamond on the server.

- In the Cell Parameters dialog, the wrong input fields were disabled for some crystal

  systems, which led in some cases to the wrong error message "Cell parameters do not

  fit with the current space group...".

- In the Symmetry dialog, short Hermann-Mauguin symbols of monoclinic space groups

  were not accepted in some cases.

- Space group recognition from symmetry matrices did not work correct. This affected

  the import of structural data from a SHELX input file.

- In the File/Open dialog, you could select the "Crystal Visualizer" format, although

  Diamond version 2 does not longer support this old file format.

Version 2.0d  -  Date of Release: 12 August 1998

- In the File/Search dialog, the "Start" button was disabled when you set the search

  directory via the "Browse" button. When you searched for elements (category Chemical

  composition), also files matched that contained no atomic parameters.

- "Broken-off" bonds (defined in the Coordination Spheres dialog) were not displayed

  properly in the Rendering mode.

- Import of XYZ format did not work correct. Now it works (atom coordinates refer to a

  pseudo-cell of a=b=c=100 Angstroems and all angles 90 degrees and space group "P1").

Version 2.0e  -  Date of Release: 25 August 1998

- Slight changes of numbers affixed with standard uncertainty ("1.2345(6)") when reading

  from a CIF file in some cases. For example "1.2345(6)" could become "1.2308(6)".

  The changes took influence on the digits behind the decimal point only.

- When reading atom cards from a SHELX file, the electron density of a Q record was

  interpreted as the second anisotropic displacement parameter, while the isotropic

  displacement parameter (mostly 0.05 on a Q record) was interpreted as the first

  anisotropic displacement parameter.

- When writing atom cards into SHELX format (using the File / Save as function), the

  site occupation factors were not written in some cases. That means the SHELX programmes

  would have read the isotropic displacement parameter as site occupation factor instead.

- System hang-up when formatting data sheet contents caused by some "illegal" combinations

  of backslash and formatting character.

- Atomic coordinates 1/3 and 2/3 on special sites were not recognized as 1/3 and 2/3, rsp.,

  if the input values were inexact. This led to the wrong Wyckoff position in the atomic

  parameter list.

- Error in the Windows resource handling when using user-defined texts in rendered mode.

  This could lead to strange results (especially font errors) when working a long time

  with a structure picture or when using the Rock'n'Roll function.

- The structure document was not marked as modified if Rock'n'Roll has been applied to

  it but no other changes were made. (The structure window was closed without request

  for saving or not.)

Version 2.0f  -  Date of Release: 15 September 1998

- When creating the symmetry-equivalent sites, in some few cases sites with similar

  coordinates were not considered to be equal. This affected especially some trigonal

  and hexagonal space groups.

- In the data sheet coordinates of some special sites were not given as fraction

  (e.g. "0.25000" instead of "1/4", or "0.33333" instead of "1/3").

- Long symmetry operations such as "-0.33333+x-y,0.66667-y,0.33333+z" were not formatted

  correctly in some cases (atom list, data sheet).

- Incomplete drawing of thick bonds in rendering mode (but not in standard mode) in some

  cases if at least one of the bonds had the attribute "Invisible".

- If a full version of Diamond was installed after the demo version, the full version ran

  in demo mode, although the key file DIAMOND.KEY was present.

- In the VRML export of the structure picture, Diamond did not make use of user-defined

  text, atom and bond labels as well as of the unit cell axes a,b,c and cell edges.

Version 2.0g  -  Date of Release: 7 October 1998

- When saving structural data or the contents of the data sheet or lists in a text format,

  the default file extension DSF was not changed to "TXT", "CSV" etc. (You had to change

  it manually before saving without overwriting the DSF file.) If the user does not

  specify an extension, this is appended automatically. To suppress appending of an

  extension, use a name ending with a dot.

- The selection of bonds was difficult if the bond's projection in the structure picture

  was (nearly) vertical or horizontal.

- In some cases, thick bonds appeared as convex polygons, if one of the connected atoms

  had a radius of (nearly) zero.

- Fragmentated bonds had not shading edge.

- When changing the space group to hexagonal, Diamond did not check for the 120 degree

  angle.

- The default bond design was not saved properly in the Diamond configuration file.

  Thus, after each restart of Diamond, bonds of new or imported structures got the

  default setting "thin bond with auto color". In some cases, "Black on white mode"

  was not restored properly after a restart of Diamond.

- When measuring distances, angles or torsion angles, Diamond did not check properly

  if the measured atom pair, triplet or quadruplet, rsp., was already in the list.

  Moreover, measured distances, angles and torsion angles were not re-calculated after

  changes of structural parameters.

- When using Undo or Redo function, the list of distances and/or angles in the data pane

  was not updated automatically.

Version 2.0h  -  Date of Release: 19 November 1998

- Coordinate triplets have sometimes been wrong formatted in the "Object Info" window, which

  displays infos about the clicked object when Object Info mode is active.

- If you used formatting symbols for individual text for atom or bond labels, these labels

  were not formatted correctly (e.g. superscripts or subscripts). If you edited or changed

  the individual text, the "Apply" button in the "Atom labels" or "Bond labels" dialog was

  not activated.

- In some cases, formulae in the data sheet were cut, e.g. "La4Ti4S4O" instead of (correct)

  "La4Ti4S4O10".

Version 2.1  -  Date of Release: 21 December 1998

- Printing of rendered pictures. Previous versions of Diamond needed a large amount of

  memory (RAM) to buffer the contents of the printout page. That was often too much for

  normal computers. The printing failed in these cases because of too low memory, or

  Diamond announces "success" but no printout left the printer.

  Diamond now uses banding for rendered printouts, that means it prints the picture in

  smaller portions that need less memory. See Help Library for details.

- Picture did not refresh after changing the page format with "File/Printer setup...".

- Axes of the coordinate system appeared ten times thicker if a thickness greater than

  zero has been set in standard mode. In rendered mode, the axes appeared only one pixel

  wide, regardless of the setting for the line thickness. The labels a,b,c or x,y,z, rsp.,

  appeared too small when printed in rendering mode.

  The positioning of the labels x,y,z or a,b,c, rsp., has been improved to reduce overlap

  with the axes.

- The alignments for labels "Left" and "Right" have been swapped to avoid misunderstandings.

- The configuration did not register changes of the model (wires, ball-and-stick, space-

  filling), projection, stereo, depth cueing, lighting, and rendering, if these settings

  were changed by use of the corresponding icons in the Display toolbar only.


Frequently Asked Questions

•	How to select and manipulate groups of atoms?

When someone wants to delete a whole group of atoms, e.g. all the hydrogens, he/she has to do that manually, one by one. It would be nice if when you say "delete" to have besides the options "atom(s)", "molecule" the option "group of atoms" so that you can delete at once all the hydrogens for example.

In former DIAMOND versions you found several menu entries to manipulate particular groups of atoms, bonds, etc. Since it is not possible to consider all combinations of groups and operations DIAMOND 2.0 follows an other strategy. The key is to switch the right info pane to a particular list of visible objects. This is done with the "List" command of the 'Display" menu. For example: "Display / List / atom types" shows a list of all atom types (i.e. combination of chemical element and oxidation state) of the current structure. Now you can select one or multiple entries of the list with the mouse. Then you open the context menu (right mouse button) and choose the command "Select atom(s)". This will select all corresponding atoms in the graphics pane. At last you should give back the focus to the graphics pane. Therefore you click on the graphics pane while pressing the <Shift> key. Now you are free to manipulate the selected atoms, e.g. delete them by typing the <Del> key.

•	Problems with printing within DIAMOND

So far I was not successful in sending rendered structure pictures directly to the printer. The preparation needs a lot of time (about 15 min., depending on the size of the structure). Finally Windows gives the message that it is unable to add it to the printer queue. The print files are obviously very large and therefore cannot be loaded.

DIAMOND creates a bitmap for the whole printing page in memory. It uses a resolution of 300 dpi and 16-Bit or 24-Bit colours, depending on the current setting of the operating system. That means, that for a 8*12 inch page DIAMOND needs 16 or 24 MBytes, respectively. In case your computer has not enough RAM, Windows swaps it to the harddisc, which slows down the processing speed. The bitmap is then transferred to the current printer driver, which also may produce space consuming temporary files. So you need a plenty of free harddisc space for printing. To speed up printing, additional RAM is useful as well as a faster processor.

•	Post-processing of rendered pictures

One of the main enhancement of Diamond 2.0 in relation to 1.2 is obviously the "rendering mode". But I was a little disappointed when I discovered that this beautiful way of structural representation was only available on the screen of my PC. [.....] and it was not possible, when you use the command "copy", to work on the picture with CorelDraw! (for example) because the copy is a bitmap one. So, there is not any possibility to "ungroup" the different object. You must work in "normal" mode to obtain a suitable picture...

The "Rendering Mode" is technically (from the developer's view) very different from the "Standard mode". In standard mode, Windows functions are used to draw objects like spheres, polygons for thick bonds etc., whereas in rendering mode, the OpenGL 3D graphics interface is used. The Windows drawing objects can be exported as 2D objects in a vector-oriented graphics format, but the 3D objects cannot! So it is unfortunately impossible to give the user the opportunity to post-process the structure picture, e.g. by ungrouping objects.

•	Problems in the import of Crystal Visualizer files from ICSD CD-ROM

I have been unable to load data files stored using the Crystal Visualizer program provided with the ICSD CD-ROM. I have tried both .Z and .ZP formats without any success.

Crystal Visualizer is an old precursor of DIAMOND 1.xx and its format was supported by the older DIAMOND versions. But this format is no longer supported by DIAMOND 2.0. To visualize structures from the ICSD (Inorganic Crystal Structure Database), export them using the CRYSTIN or CIF format (use 'Export' command from 'File' menu within RETRIEVE). These formats can directly be loaded into DIAMOND and you can start to build up new structure models.

•	Difficulties in finding the correct space group in the Collapsible tree

For the novice crystallographer, it is VERY difficult to find the correct space group in the Collapsible Tree. (i.e. I spent quite a while looking for the P21/A space group). It would be helpful if I could remove the collapsible tree of space groups and alphabetize ALL SPACE GROUPS in a single list not just those in the outer shell.

When you type in the required space group symbol and then switch to the list by pressing the <TAB> key, the program automatically jumps to the symbol, so in fact you don't have to search it.


Tutorial: Overview
Tutorial Overview

This tutorial will help you to manage DIAMOND. Though a graphical user environment like MS Windows 95 (or 98) or Windows NT simplifies and standardizes the usage of computer programs, DIAMOND is a complex tool for complex tasks and therefore it is not completely trivial to use. Even an experienced Windows user should familiarize with the basic Elements within this chapter.

But we must assume that you are familiar with Windows. This tutorial is no manual for computer beginners.

The tutorial has three chapters. In the first chapter you will learn the basics of handling with the help of a prepared structure file. You will be told how to bring the expected structural part into the right position. In the second chapter you will get to know DIAMOND’s several potentialities to represent a structure. The third chapter finally will tell you how to present even complex structures in a few steps.


Tutorial: First Steps
First Steps

In section #1 you will learn:

•	How to read structure files, which have been edited by DIAMOND.

•	How the contents of a structure window are arranged and where to find which informations about the structure.

•	How to change the orientation of the structure model.

•	Which variations of representations DIAMOND can use to display a structure.

Opening a File

	Click on the “Open” button in the standard toolbar. Choose the directory “Samples\Tutorial”, and then double click on the file with name “Quartz.dsf”.

In the left area of the window, you will find the structure picture, whereas textual informations are provided in the right area. This is by default the so-called data sheet, but there may also be a table of atoms, bonds, or other objects, instead. You can shift the border (the so-called “splitter”) between these two areas with the mouse.

Rotating and Shifting the Structure

	1. Click on the “Rotation X/Y” button. The mouse cursor will change its standard arrow symbol. If you now press down the left mouse button and move the mouse with left button down, the structure will rotate corresponding to the movement along x- and y-axis. (Both axes are located in the screen area. The x-axis points toward right, the y-axis up.)
	2. Click on the “Rotation Z” button. Like for the rotation along x- and y-axis, you can now rotate the structure along the z-axis. (The z-axis is perpendicular to the screen and points toward you.)
	3. Click on the “Shift” button. Now you can shift the structure within the window, while the left mouse button is pressed down.
	4. Now click again on the “Rotation X/Y” button. You will notice that the structure does not rotate along the center of picture but along its center of gravity.
	5. Click on the “End Tracking Mode” button to return to the normal mode. Instead you can press the <Escape> key.
Moving the center of rotation

	1. Select the uppermost Si atom by clicking on it with the mouse. Then click on the “Center of rotation” button. DIAMOND will move the center of rotation to the position of the selected atom.
	2. Click on the “Rotation X/Y” button. Now the structure can be rotated along the new center of rotation.
	3. Click on the “End tracking mode” button to return to the normal mode.
	4. Now select two neighbouring Si atoms by clicking on the atoms one after the other with the <Shift> key pressed down. Then click on the “Center of rotation” button. DIAMOND puts the center of rotation into the center of both selected atoms.
	5. Now click again on the “Rotation X/Y” button. The structure can now be rotated along the new center of rotation.
Changing Enlargement Factor

	1. Click on the “Enlargement factor” button. Again the mouse cursor will change its symbol. With left mouse button pressed down, the enlargement factor can now be varied by moving the mouse.
	2. If you want to enlarge a detail of the structure picture, click on the “Zoom” button, and then, with left mouse button pressed down, draw up a frame around the detail of interest. After you have released the left mouse button, DIAMOND enlarges the detail to fill out the entire structure window.
	3. You can use the “Center+Adjust” button to adjust the enlargement factor so that the entire structure picture fits into the structure window. This function also moves the center of rotation into the center of the structure. This function can be called using the <F9> key, instead.
Models

To visualize a three-dimensional chemical structure, various models have proved successful:

	1. The wire model displays only the bonds that are defined in the structure, while the atoms are represented by the terminal points of the bonds. This model requires defined bonds, a condition that is often not fulfilled, even in inorganic compounds. It allows a very good overview on the bonding geometry and is the method of choice for molecular structures, but the space filling of a structure cannot be represented.
	2. In the ball-and-stick model atoms are represented as spheres, and bonds are drawn as sticks or lines. This is the standard model of DIAMOND. By variation of the atomic radii an optimal overview on geometric relationships can be adjusted as well as on space filling aspects.
	3. The space-filling model does not show any bonds but atoms only, where van-der-Waals radii are used so that the spheres touch or interpenetrate. This model allows a good impression of the space filling aspects of the structure, whereas constitutions and coordination relationships are difficult to recognize.
	4. All mentioned models can be displayed either flat or rendered. The rendered mode offers a more realistic representation, while the flat mode works significantly faster, especially when rotating the structure.

From left to right: Quartz structure in wire, ball-and-stick, and space-filling model,

each in flat (first row) and rendered mode (second row)

Thermal ellipsoids and Coordination Polyhedra

	A special variant of the ball-and-stick model are the so-called thermal ellipsoids. They represent the displacement of the atoms caused by thermal vibrations. Therefore informations from the so-called anisotropic displacement parameters are needed.
	Coordination polyhedra can be used to characterize the atoms' neighbourhoods. Therefore, local coordinations are symbolized by geometric polyhedra, whose orientation to each other may represent higher coordinations. Like for thermal ellipsoids, coordination polyhedra are a variation of the ball-and-stick model in DIAMOND. To select coordination polyhedra, select the corresponding central atom by mouse click, and then click on the “Add polyhedra” button.

Quartz structure with thermal ellipsoids (left) and polyhedra (right),

each in flat (first row) and rendered mode (second row)

Perspective

Normally DIAMOND displays structures using the so-called parallel projection. That means looking at the structure from infinite distance and can be compared with observing a far away object using binoculars. Thus, parallel projection leads to a parallel display of parallel lines.

But in fact nobody does permanently observe his environment with a binocular. The natural way means a ‘real’ distance from the observed object and is better described with the so-called central projection. This projection leads to a non-parallel display of parallel lines, which makes it difficult to understand the geometrical relationships.

	DIAMOND supports both ways of projection and allows a comfortable switching between them using the shown button.
Stereoscopic Projection

A real 3-dimensional impression is obtained by a stereoscopic projection. Therefore the structure is drawn twice side-by-side, where each is rotated before around the y-axis of the view coordinate system for the stereo angle (the left picture in positive direction, the right picture in negative direction).

	DIAMOND switches between normal and stereoscopic projection if you press the given symbol in the toolbar.

Note that for a correct stereoscopic projection central projection is also necessary, so central projection should be enabled.

For the inspection of a stereo picture stereoscopic glasses should be used. Those glasses separate both pictures by a system of mirrors. But with some practice a stereo picture can also be inspected without such aid. Look between both pictures and focus to an infinite point (try to squint a little bit). Doing so a third picture, which is 3-dimensional, appears between the others.


Tutorial: Building up Structures: Overview
Building up Structures: Overview

In section #2 you will learn:

•	How to input or change structural data or read data from foreign file formats.

•	How to create simple structural parts by filling of cell ranges.

•	How to study structural details by stepwise building up of coordination spheres.

•	How molecular structures can be displayed automatically by DIAMOND.

•	How to present complex coordinations with the aid of polyhedra.


Tutorial: Building up Structures: Cesium Chloride Structure
Building up Structures: Cesium Chloride Structure

DIAMOND imports crystal structure data automatically from all common file formats. But if a structure should not be available in electronic form, you can enter these data manually.

With the example of the simple cesium chloride structure, this will be demonstrated here.

Entering structure data

1. Click on the “New” button in the standard toolbar. DIAMOND will then open a structure window using default values for space group (P1) and unit cell (cell lengths = 1 Å, angles = 90°).

2. Now choose the “Symmetry” command from the “Edit” menu to open the “Symmetry” dialog. Enter the Hermann-Mauguin-Symbol “P m -3 m”, or select the symbol from the list below. Confirm with “OK”.

3. Then choose the “Cell” command from the “Edit” menu to open the “Cell” dialog. Since a cubic space group has been selected, the specification of one cell length value (a = 4.115 Å) is sufficient. All other values derive from the cubic geometry.

4. Finally choose the “Atomic parameters” command from the “Edit” menu to open the “Atomic parameters” dialog. Here you will enter the atoms of the asymmetric unit.

5. Click on the “Append” button, and enter the following details into the corresponding fields. Repeat this for each atom of the asymmetric unit.

Element	Symbol	Oxidation no.	SOF	X	Y	Z
Cs	Cs 1	+1	1.0	0	0	0
Cl	Cl 1	-1	1.0	1/2	1/2	1/2

6. Close the dialog with “OK”. In the data sheet on the right part of the structure window, all changes will be documented.

Now you have entered all necessary data for the structure. Further, bibliographic data will be used only for documentation and are not mandatory for the structure modelling.

For new structures or structures with data imported from foreign file formats, the corresponding structure window is at first empty in principle. DIAMOND offers a multitude of strategies to build up a structural part. But you have to decide, how to lead your way.

The simplest way is to display the contents of the unit cell. This is the method of choice especially for structures with high symmetry, which do not contain too many different chemical elements. In many cases, larger ranges of the structure, consisting of multiple cells (the so-called “super cell”) will be more successful.

Filling a Cell Range

	1. Click on the “Add cell edges” button to generate and display the borders of the unit cell.
	2. Click on the “Fill unit cell” button. DIAMOND now creates all atoms within the borders of the unit cell. In the center of the cell you will see a chlorine atom, which is surrounded by eight cesium atoms in the corners of the cell. For a better representation of the coordination of the cesium atoms, you will now generate a bigger structural part.
	3. Choose the “super cell” command from the “Fill” submenu of the “Structure” menu to open the “Fill super cell” dialog, where you choose the option “2 x 2 x 2 cells”. Additionally switch on the “Create cell edges automatically” setting, and then confirm with “OK”. DIAMOND will then create a total number of eight cells including the accessory cell edges:


Tutorial: Building up Structures: Graphite Lattice
Building up Structures: Graphite Lattice

The carbon modification graphite will serve as a simple example how to model layer structures by stepwise building up of coordination spheres.

In the first step, the structural part will be built up.

	Click on the “Open” button in the standard toolbar. From the File Open dialog, choose the directory “Samples\Tutorial”, and double click on the file with the name “Graphite.dsf”.
Filling a Cell Range

	1. Click on the “Add cell edges” button. DIAMOND will then generate and display the edges of the unit cell. You can easily recognize the rhombohedral geometry.
	2. Click on the “Fill unit cell” button. DIAMOND will generate all atoms within the unit cell, in this case only two carbon atoms. Assert that the ball-and-stick model has been selected. Otherwise (in wire model) atoms will only be displayed as dots.
Completing Coordination Spheres

	1. Click on the “Coordination spheres” button. DIAMOND will then research the coordination sphere of every atom for neighbouring atoms up to the preset bonding distance and connect the center of the coordination sphere with its neighbours. Repeat this step five times.
	2. Click on the “Center+Adjust” button to adjust the structural part, which has become quite large, to the window dimensions.

In the second step, the positions of the carbon layers relative to each other will be visualized. Therefore, the two structural parts will be colored differently and then projected in a suitable orientation.

Changing Atom Colors

	1. With the right mouse button, click on an arbitrary atom of the upper structural part. This will open a so-called context menu next to the mouse cursor. From this context menu, choose the “Select molecule(s)” command. DIAMOND will then determine all atoms that are connected with the selected atom by a recursive search, and select these atoms.
	2. Once again, click with the right mouse button on one of the selected atoms, and choose the “Edit atom(s)” command from the context menu. In the “Edit atoms” dialog, choose the “Interior color” Green. Confirm with “OK”. Then all selected atoms will become green.
	3. Repeat the previous two steps with the lower structural part. But now choose the color blue.
	4. Click on the “Wire model” button to change from the ball-and-stick model to the wire model. DIAMOND will now display bonds only, but with the colors of the connected atoms.
	5. Click on the “Perspective” button to change from central to parallel projection.
	6. Finally, choose the “Rotate” command from the “Display” menu. Use the “Rotate structure” dialog to rotate along the x-axis for 90 degrees. The result illustrates the honey-comb pattern of the atoms of one layer as well as the staggered arrangement of the layers to each other very well.


Tutorial: Building up Structures: Hittorf's Violet Phosphorus
Building up Structures: Hittorf's Violet Phosphorus

The violet modification of phosphorus has a rather complicated crystal structure. For a better understanding how the structure is built up, the coordinations will be researched step by step, beginning with one single starting atom.

Creating the Initial Atom

	1. Click on the “Open” button in the standard toolbar. In the File Open dialog, choose the directory “Samples\Tutorial”, and double-click on the file with the name “Hittorf.cry”. This file originates from the Inorganic Crystal Structure Database (ICSD) and will be converted automatically.
	2. Click on the “Add atoms” button, which opens the “Add atoms” dialog. From the atomic parameter list, choose the last entry (P 21), and then confirm with “OK”. DIAMOND will then generate one single phosphorus atom.
	3. Click on the “Center of rotation” button. This will bring the previously created phosphorus atom into the center of rotation as well as into the window's center.
Completing Coordinations Spheres

	1. Click five times after each other on the “Coordination spheres” button. DIAMOND will complete the coordinations of the structural part step by step.
	2. Now orientate the structure with the mouse, leading to the picture given below. The resulting fragment consists of two approximately pentagonal tubes, which are situated perpendicular to each other and connected via a bridging atom.
	3. Choose the “Coordination spheres” command from the “Structure” menu to open the “Fill coordination spheres” dialog. Set the input field “Number of cycles” to 20, and then confirm with “OK”. DIAMOND will now complete the coordination sphere of the fragments for totally twenty times.

After this procedure, you will realize the arrangement of a double layer with crossed pentagonal tubes. Multiple of such layers make up the crystal structure. To illustrate the arrangement of the layers to each other, the structure will now be built up once again.

Deleting a Structure

Select the entire structural part with <Ctrl+A>, and then press <Del>. This will delete all parts of the structure picture.

Filling a Cell Range

	1. Click on the “Add cell edges” button. DIAMOND will then generate and display the edges of the unit cell.
	2. Choose the “View” command from the “Display” menu to open the “View” dialog. Orientate the structure with view (1,1,0). For that, enter “1” into the first and second input field besides “u,v,w”, and “0” into the last input field. Then click the “Set” button. Then close the dialog with “Close”.
	3. Click on the “Fill unit cell” button. DIAMOND will “fill” the unit cell, which means it will generate all phosphorus atoms in the unit cell.
Completing Coordination Spheres

	Click five times after each other on the “Coordination spheres” button. DIAMOND will complete the environment of the structural part step by step.

You will make out an upper and a lower structural part, which is symmetrical to the upper one. Really each of these two structural parts consist of two further subunits, which are interlocking but not connected with each other.

To emphasize this, the structural parts will now be colored differently.

Changing Colors of Structural Parts

1. Click with the right mouse button on an arbitrary atom of the middle tube of the upper part. Next to the mouse cursor, the context menu will open, where you choose the “Select molcecule(s)” command. DIAMOND will now recursively select all atoms, which are connected with the previously selected atoms.

2. Now click again with the right mouse button on one of the selected atoms, but choose the “Edit atoms” command from the context menu. Assign a green color to the selected atoms.

3. Repeat steps 1 and 2 with the analogous fragment in the lower half of the structure.

Now you can make out very well, how this modification of phosphorus is built up, especially when rotating the structure.

Now you can make out very well, how this modification of phosphorus is built up, especially when rotating the structure.


Tutorial: Building up Structures: Sulfur
Building up Structures: Sulfur

The element sulfur exists in a variety of modifications, where the monoclinic gamma modification is one of the most known. In this modification, sulfur is built up of packed, crown-shaped eight-membered rings. This example will demonstrate, how DIAMOND can work with molecular structures.

	1. Click on the “Open” button in the standard toolbar to open the File Open dialog. Choose the directory “Samples\Tutorial”, and double-click on the file with the name “Sulphur.dsf”.
	2. Click on the “Add cell edges” button, where upon DIAMOND will generate and display the edges of the unit cell.
Creating Molecules

	1. Click on the “Molecules” button. DIAMOND will now attempt to isolate one or more molecular substructures from the atomic parameter list by a recursive search for neighbouring atoms. In this example, DIAMOND will find two ring-shaped sulfur molecules in different orientations. We will see that these two substructures are representative for the complete crystal structure. For that we will generate a so-called packing diagram.
	2. Click on the “Fill unit cell” button. DIAMOND will “fill” the unit cell with sulfur atoms.
	3. Click on the “Connect” button. DIAMOND will connect all displayed atoms on the basis of the currently defined bond criteria (connectivity). It will turn out that some molecules seem to tower above the borders of the unit cell, and only the corresponding fragments have been built.
Completing Fragments

	1. Click on the “Fragments” button. All molecular fragments will be completed.
	2. Finally click on the “Perspective” button to change to parallel projection. The result is a packing diagram, which clearly shows the stacking of the sulfur molecules.


Tutorial: Building up Structures: Phosphorus Pentoxide
Building up Structures: Phosphorus Pentoxide

Similar to sulfur, phosphorus pentoxide consists of molecular units. This simple, binary structure will help to introduce the usage of coordination polyhedra.

	Click on the “Open” button in the standard toolbar to open the File Open dialog. Choose the directory “Samples\Tutorial” and double-click on the file with the name “P4O10.cry”.
Creating Molecules

	1. Click on the “Molecules” button. DIAMOND will find one single P4O10 molecule. Assert that the ball-and-stick model has been selected, and rendered representation, lighting, and parallel projection have been activated.
	2. Click on the “Center+Adjust” button to adjust the structural part into the window's dimensions.

Now the coordination of the oxygen atoms around the phosphorus atoms shall be displayed with the aid of coordination polyhedra. The ligand atoms (here: oxygen) will therefore be abstracted to the corners of convex polyhedra.

In DIAMOND, you can freely determine, up to what distance ligand atoms will be consulted for the creation of polyhedra. For that either ‘fixed’ or ‘generic’ spheres will be used. Fixed spheres are defined as constant distance interval independent from the atom types concerned. Generic spheres are derived for each atom type individually from the current connectivity list.

Creating Polyhedra

1. Choose the “Polyhedra” command from the “Objects” menu to open the “Add polyhedra” dialog. Select phosphorus (P) as central atom and oxygen (O) as ligand atom. Set the sphere type to “Generic”.

2. Additionally define the design of the polyhedra to be created by clicking the “Design...” button. In the “Design for new polyhedra” dialog, check the “Use central atom's main color as Interior color” checkbox. Choose "blue" for the polyhedron edges, "solid" pen, and a thickness of "0.5".

3. On the “Material” page of the dialog, set the value for “Transparency” to 0.5.

4. Finally, press the “Options...” button to open the “Global settings for polyhedra” dialog, where you set the “Ligand atoms reducing factor” to 0.01. This factor results in a reducing of all atoms on the corners of the polyhedra to indiscernible size.

5. If you now close all open dialogs with “OK”, DIAMOND will create four transparent tetrahedra, which are connected via corners.


Tutorial: Building up Structures: Keggin Structure
Building up Structures: Keggin Structure

The anions of a heteropoly acid will serve as a complex example for the use of polyhedra.

	Click on the “Open” button in the standard toolbar to open the File Open dialog. Choose the directory “Samples\Tutorial” and double-click on the file with the name “Keggin.cry”.
Creating Initial Atom

	1. Click on the “Add atoms” button to open the “Add atoms” dialog. Select the first atom (P 1) from the parameter list, and then confirm with “OK”. DIAMOND will create a single phosphorus atom.
	2. Click on the “Center of rotation” button and assert that the ball-and-stick model has been selected. (In wire model, all atoms would be displayed as dots only.) The phosphorus atom should now be positioned in the center of the structure picture.

Building up coordination spheres using ‘generic’ distance intervals requires the appropriate setting of the connectivity. By default, all atom types, which have oxidation states with different signs (cations and anions), are considered to be potentially connected. The connecting distance interval is made up of the sum of the effective ionic radii.

This default setting supposes ‘ideal’ conditions and needs to be corrected in many ‘real’ structures. Therefore it is recommended to check the connectivity for every structure that has been imported from a foreign file format.

Checking Connectivity

	Click on the “Connectivity” button to open the “Connectivity” dialog. The preset connected atom types are: “P+5 - O-2”, “W+6 - O-2”, and “O-2 - H+1”. Now select the bonding sphere for “W+6 - O-2” from the combo box “Bonding sphere”. Since the preset bonding sphere for “W+6 - O-2” is too small, change the “DMax” value to a value about 3.0 Å. Then confirm the settings with “OK”.
Completing Coordination Spheres

	Click on the “Coordination spheres” button. DIAMOND will find four oxygen atoms in tetrahedral coordination in the neighbourhood of the phosphorus atom.
Creating Polyhedra

	1. Choose the “Polyhedra” command from the “Objects” menu to open the “Add polyhedra” dialog. Select phosphorus (P) as central atom and oxygen (O) as ligand atom. Set the type of sphere to “Generic”.
	2. Click on the “Design...” button to open the “Design for new polyhedra” dialog. Choose “Purple” as interior color and set the edges' thickness to 0 mm. On the “Material” page, set the value for “Transparency” to 0.
	3. Confirm all dialog boxes with “OK”. DIAMOND will now create a purple tetrahedron around the central phosphorus atom.

Now another coordination sphere will be examined.

Completing Further Coordination Spheres

	1. Click on the “Coordination spheres” button. DIAMOND will find another twelve tungsten atoms beyond the PO4 tetrahedron.
	2. Click once again on the “Coordination spheres” button. DIAMOND will find another sphere consisting of oxygen atoms, which surround the tungsten atoms approximately in octahedral form.
Creating Polyhedra

	1. Choose the “Polyhedra” command from the “Objects” menu to open the “Add polyhedra” dialog.
	2. Click the “Design...” button to open the “Design for new polyhedra” dialog. Choose the interior color “Blue” and leave the other settings as before.
	3. Confirm all dialog boxes with “OK”. DIAMOND will now create a blue octahedron around the central tetrahedron.

Changing the orientation manually should lead to the picture shown above. You see, only a few mouse clicks have been necessary to learn and visualize these complex coordinations step by step.


Tutorial: Special Techniques: Overview
Special Techniques: Overview

In section 4 you will learn:

•	How to present even complex structures in a few steps.

•	How to apply filter, dummy atoms and selections effectively.

•	How to create crystal surfaces with defined orientation easily.

•	How to present proteins quickly.


Tutorial: Special Techniques: Zeolite Framework such as Faujasite
Special Techniques: Zeolite Framework such as Faujasite

Faujasite is a famous representative of the zeolites. One of the components in the linking pattern of this aluminosilicate is the so-called “beta-cage”. You must imagine one silicon or aluminium atom in each of the corners of the polyhedron. Each edge stands for an oxygen atom, which links two atoms in the corners. The beta-cages are connected with each other via hexagonal prisms.

In the first step you will model one single beta-cage:

	Click on the “Open” button in the standard toolbar to open the Open File dialog. Select the directory “Samples\Tutorial” and double-click on the file with the name “Faujasite.cry”. As usual, DIAMOND will open a structure window, which is empty at the beginning.
Creating an Initial Atom

	1. Click on the “Add atom(s)” button to open the “Add atoms” dialog. Select the atom “Si 1” from the parameter list and leave the other settings as before (see figure). Confirmation with “OK” will create a single atom, but still positioned outside the view.
	2. Assert that the ball-and-stick model has been selected. (In wire model, atoms will be displayed as dots only.) Click on the “Center of rotation” button. The created atom should now be visible in the center of the structure picture.

Since only the connection between the Si and Al atoms is of interest in our example, it is expedient to lock out all other atom types from the construction until further notice. In DIAMOND, this will be done with a filter.

Editing Filter

	Click on the “Filter” button to open the “Filter” dialog. In the “Atom types” list, remove all selections but that for “SiAl”. Additionally, remove all selections but “+(0,0,0)” from the “Bravais translations” list. If you now confirm with “OK”, only atoms of the mixed site Si/Al will be created, and no Bravais translations will be applied. To remind you of the active filter, DIAMOND displays a warning symbol in the lower left corner of the structure window.

Since our structure model is designed to have direct connections between Si/Al atoms, which makes no chemical sense of course, the connectivity needs adjusting.

Checking Connectivity

	Click on the “Connectivity” button to open the “Connectivity” dialog. In the list “Atom type pair(s) to be connected”, remove all selections but that for the atom type pair “SiAl - SiAl”. Now define a bonding sphere of approximately 3.0 to 3.5 Å in the lower half of the dialog box.
Completing Fragments

	Click on the “Fragments” button. DIAMOND will complete the fragment and generate a beta-cage as well as four attached hexagonal prisms. By means of the active filter, only Si/Al atoms will be created, and the recursive search for neighbouring atoms will be cancelled because of the locked out Bravais translations.

In the second step, the beta-cage will be displayed as closed polyhedron. Since all polyhedra require a central atom in DIAMOND, such a central atom must be defined now. If the structure in use does not have any appropriate atom type that can be used as central atom, we can add a so-called “dummy atom”.

Inserting a Dummy Atom

	1. At first change the orientation leading to a view along the cubic diagonal of the unit cell (1,1,1). For that choose the “View” command from the “Display” menu to open the “View” dialog. In the three input fields next to “u, v, w” enter “1”, and then push the “Set” button. (DIAMOND will change the view now.) Then close the dialog box.
	2. Press the key combination <Ctrl+A> to select all objects of the picture. Then choose the “Insert atom” command from the “Structure” menu. This will open the “Insert atom” dialog. DIAMOND has calculated the center of all selected atoms and proposes this center as position for a dummy atom. In our example, this position is exactly (1/8, 1/8, 1/8). Confirm with “OK”. Then press the <Esc> key to reset all selections in the structure picture. Now there is a dummy atom in the center of the structure, which can be used as central atom for a polyhedron. In the data sheet (in the right part of the structure window), you will see a new entry for the dummy atom in the atomic parameter list.
Creating Polyhedra

	1. Choose the “Polyhedra” command from the “Objects” menu to open the “Add polyhedra” dialog. Select “?” as central atom type and “SiAl” as ligand atom type. Set the type of sphere to “Fixed” and “RMin” to 1 and “RMax” to 5.
	2. To define the design of the polyhedra to be created, click on the “Design...” button. In the “Design for new polyhedra” dialog define settings as given in the figure. On the “Material” page the value for “Transparency” should be zero.
	3. Finally you should click the “Options...” button to open the “Global settings for polyhedra” dialog. Set the “Ligand atoms reducing factor” to 0.01. This factor results in a reducing of all atoms on the corners of the polyhedra to a size which is rather indiscernible but still ready to be selected. If you close all open dialog boxes now with “OK”, DIAMOND will create the polyhedron.

In the third step, the hexagonal prisms, which connect the beta-cages, will be displayed as polyhedra, too. For that, we use a similar strategy like for the beta-cage itself.

Inserting a Dummy Atom

	1. Again we will change the orientation in a suitable way. Choose the “Rotate” command from the “Display” menu to open the “Rotate structure” dialog. Enter a value of 30 degrees for the z-axis and assert zero for both x- and y-axis. Then click on the “Apply” button. This will cause the desired rotation without closing the dialog. Now set the value for the z-axis to zero, but that for the x-axis to -20 degrees. Then confirm with “OK”.
	2. Select all atoms of the prism that points at the bottom by pulling up a frame around the atoms concerned.
	3. Then choose again the “Insert atom” command from the “Structure” menu. DIAMOND will calculated the center of all selected atoms and will now propose the position (1/4, 1/4, 1/4) for a dummy atom. Confirm with “OK”. Then press the Escape key to reset all selections in the structure window. This has inserted another dummy atom into the center of the lower prism. The data sheet in the right part of the structure window displays the new dummy atom in its atomic parameter list, too.

The central atoms of the other prisms need no further dummy atom in the list of atomic parameters. They can be generated from the previously inserted dummy atoms using suitable symmetry operations.

Creating Polyhedra

For this procedure, the filter needs to be adjusted first.

	1. Click on the “Filter” button to open the “Filter” dialog. Lock out all atom types except “?”, which represents the two dummy atoms from the list “Atom types”. Click the “Mark all” button below the list of symmetry operations. This will select all Bravais translations.
	2. Choose the “Spheres” command from the “Structure” menu to open the “Define fixed sphere” dialog. Set “RMin” to 0 and “RMax” to 4 [Å]. After you have confirmed with “OK”, DIAMOND starts to search all missing dummy atoms, which have a maximum distance of 4 Å from the Si/Al atoms. This will generate one dummy atom in the center of each hexagonal prism. Now the polyhedra can be created. But before that the Si/Al atoms must be unlocked from the filter.
	3. Click on the “Filter” button to open the “Filter” dialog. In the list “Atom types” select “SiAl” additionally to “?”.
	4. Choose the “Polyhedra” command from the “Objects” menu to open the “Add polyhedra” dialog. Select the atom type “?” for the central atoms and “SiAl” for the ligand atoms. Set the type of sphere to “Fixed” and “RMin” to 1 and “RMax” to 5.

In the fourth and last step, the connection of the -cages with each other will be visualized.

For that, change the orientation again viewing along the (1,1,1)-axis:

Choose the “View” command from the “Display” menu, and set the input fields next to “u,v,w” to 1, then confirm with “Set”, then close the dialog box.

Completing Coordination Spheres

	1. Choose the “Spheres” command from the “Structure” menu to open the “Define fixed sphere” dialog, and define a sphere of 0 to 5 Å this time. Confirm with “OK”.
	2. Click twice on the “Fixed spheres” button. This will execute the search for neighbouring atoms for two other times with the previously set search radius.
	3. Click on the “Center+Adjust” button to adjust the structural part, which has become quite large, to the window's dimensions.
Creating Polyhedra

	Choose the “Polyhedra” command from the “Objects” menu to open the “Add polyhedra” dialog. Do not change the previously made settings, and confirm with “OK”.

The structural part being displayed gives a quite good impression how the structure of faujasite is built up. You may extend the given structural part using the previously described operations (first complete spheres, then create polyhedra) as much as you like.


Tutorial: Special Techniques: Alpha-Boron
Special Techniques: Alpha-Boron

The crystal structure of boron consists of icosahedron units, which are connected with each other via delocalized bonds with two electrons between three centers. Again, dummy atoms can be used for the visualization.

In the first step, you will get a rough sketch of the structure.

	Click on the “Open” button to open the file “Boron.cry” in the directory “Samples\Tutorial” from the File Open dialog. This file comes from the Inorganic Crystal Structure Database and will be converted automatically. As usual for an imported structure, the structure window is empty at the beginning. Assert that the ball-and-stick model has been selected.
Filling a Cell Range

	1. Choose the “cell range” command from the “Fill” submenu of the “Structure” menu to open the “Fill cell range” dialog and enter the values given in the figure. Confirm with “OK”. DIAMOND will now generate a part of the lattice consisting of 4 x 4 cells in the xy-plane.
	2. Choose the “Rotate” command from the “Display” menu to open the “Rotate structure” dialog, enter a value of 90 degrees for the x-axis, and zero for both y- and z-axis. Confirm with “OK”.
	3. Click on the “Add cell edges” button to insert the edges of the unit cell.
	4. Click on the “Center+Adjust” button to fit the picture within the window frame.
Extracting Layers

	1. Select the two layers in the middle by pulling up a frame around the desired area with pressed left mouse button.
	2. Choose the “Invert selection” command from the “Edit” menu. This selects all atoms of the two outer layers.
	3. Press the <Del> key. This will delete all selected atoms.

In the second step, the boron icosahedra will be created. Since no central atoms exist for these polyhedra, dummy atoms will be created for that purpose.

Inserting Dummy Atoms

1. Choose the “Atomic parameters” command from the “Edit” menu to open the “Atomic parameters” dialog. Click on the “Append” button to define a dummy atom at position (0,0,0). Enter zero for “X”, “Y”, and “Z”. Then confirm with “OK”.

2. Choose the “cell range” command from the “Fill” submenu of the “Structure” menu to open the “Fill cell range” dialog, and enter the values given in the figure. Then confirm with “OK”. DIAMOND will create dummy atoms in the centers of the boron icosahedra.

Creating Polyhedra

1. Choose the “Polyhedra” command from the “Objects” menu to open the “Add polyhedra” dialog. Select the atom type “?” as central atom and boron as ligand atom. Set the type of sphere to “Generic”. Then confirm with “OK”. (For the following pictures we use yellow as interior color of the polyhedra.)

2. Select the upper layer of polyhedra by pulling up a frame around the corresponding atoms with the mouse.

3. Click with the right mouse button on one of the selected central atoms to open the context menu. From the context menu, choose the “Edit polyhedra” command, which opens the “Edit polyhedra” dialog.

4. Assign another color to the selected polyhedra, and then confirm with “OK”.

5. Return to the standard orientation (view along z-axis) by choosing the "View" command from the Display menu and pushing the "z" button in the View dialog and then closing this dialog.

In the third step, the two-electrons-three-center bonds will be displayed. For that, dummy atoms will be used to define the ‘third atom’ for each bond.

Inserting a Dummy Atom

1. In the environment of the lower left corner of the unit cell, select a total number of three adjacent boron atoms, which are involved in one of the delocalized bonds. (For that, hold the Shift key pressed down, while you are clicking multiple atoms with the mouse. For a better matching of the three atoms, you should increase the enlargement factor of the picture, e.g. by pressing the End key.)

2. Choose the “Insert atom” command from the “Structure” menu, which opens the “Insert atom” dialog, and confirm with “OK”. DIAMOND will now insert another dummy atom into the structure picture (and into the atomic parameter list). This dummy atom will serve as center of the three-center bond.

With the use of the symmetry operations, the other ‘voids’ will become occupied with dummy atoms:

3. Choose the “cell range” command from the “Fill” submenu of the “Structure” menu.to open the “Fill cell range” dialog, and enter the values given in the figure. Then confirm with “OK”.

Since the dummy atoms serve as connecting points but should be invisible, the radius for the dummy atom type will now be reduced:

4. Choose the “Atom types” command from the “Edit” menu to open the “Edit atom types” dialog. Select the atom type “?” and change to the “Radii” page. Set the value for “Drawing radius for ball-and-stick model” to 0.01. Then confirm with “OK”.

Creating Bonds

1. Choose the “Bond types” command from the “Edit” menu to open the “Edit bond types” dialog. Select the bond type "B - ?", change to the “Design” page, and set “Style = Thick; Radius = 0.05; Fragmentation = 4”. Then confirm with “OK”.

	1. Click on the “Connectivity” button to open the “Connectivity” dialog. Select exclusively the atom type combination dummy/boron (“? - B”), and change the “DMax” value to 1.5 [Å].
	2. Click on the “Connect” button to connect all atoms with each other.
	3. Click on the “Destroy non-bonded atoms” button to delete all atoms that are not involved in bonds. Structure of  alpha-boron with delocalized 2e3c bonds


Tutorial: Special Techniques: Protein Structures
Special Techniques: Protein Structures

DIAMOND is a specialist for inorganic structures. Naturally it can also deal with crystal structures that describe molecular units, which is normal in organic chemistry and biochemistry. We will demonstrate how macromolecular structures can be processed using the structure of cytochrome C as an example.

In the first step, we will give you a survey of the protein.

	1. Click on the “Open” button to open the File Open dialog, where you open the file “Cytochrome.pdb” from the “Samples\Tutorial” directory. The file comes from the Brookhaven Protein Data Bank and will be converted automatically.
	2. Click on the “Connectivity” button to open the “Connectivity” dialog. As usual, the bonding criteria should be checked at first and adjusted if necessary. Therefore click on the “Evaluate” button. DIAMOND will now adjust all atom type combinations with the internal list of mean covalent bond lengths. This process will take some seconds due to the big number of atoms in the parameter list. Confirm the (new) settings with “OK”.
	To survey the entire structure, we could start the automatic search for molecular substructures (using the “Molecules” button, as we did some times before). But this process may last a rather long time for very large molecules. Since the process works with a recursive algorithm, it may stop before the complete molecule has been found.
	Since the atomic parameter list contains one or more complete molecular units in this kind of data files, it is easier to generate one atom each from every atom of the parameter list. This could be done with the “Add atoms” dialog (“Add atoms” command from the “Structure” menu) by selecting all atoms in the parameter list, or quite simple using the “Add all atoms” function:
	3. Click on the “Add all atoms” button. DIAMOND generates all atoms of the parameter list without applying symmetry operations, Bravais translations, and integer cell translations.
	4. Click on the “Connect” button to connect all atoms with each other corresponding to the currently defined bonding spheres.
	5. Click on the “Center+Adjust” button to adjust the picture to the window's dimensions.

Some atoms have not been connected. These atoms are oxygen atoms that belong to water molecules. (H atoms have not been localized.)

	6. Click on the “Destroy non-bonded atoms” to delete these oxygen atoms.

The current version of DIAMOND does not offer protein-specific capabilities to represent the secondary structure or to differentiate for amino acids, for example. Nevertheless, some of these typical capabilities may be simulated with a few flicks of the wrist.

In the second step, we will display the so-called -C-chain.

1. Choose the “atomic parameters” command from the “List” submenu of the “Display” menu. This will change the data sheet in the right part of the structure window to a list of the atoms of the parameter list.

2. Sort the list for atom symbols by clicking on the “Symbol” tab in the list header.

All alpha-carbon atoms have the symbol “CA” and will be arranged one below the other after sorting.

3. Select all atoms with the symbol “CA”. For that, click on the first corresponding entry in the list, then scroll with the mouse to the last corresponding entry, press down the <Shift> key and then click on this last entry with the left mouse button. Now all atoms with the symbol “CA” are highlighted with blue color.

	4. Now click with the right mouse button into the selected entries, and choose the “Select atom(s)” command from the context menu. After that all alpha-C-atoms will be selected in the structure picture.
	5. Click with Shift key pressed down at an arbitrary position in the background of the structure picture. This will return the input focus to the structure picture without losing the selection in the atomic parameter list.
	6. Choose the “Invert selection” command from the “Edit” menu. DIAMOND will now reverse the selection. This means all atoms but the alpha-carbon atoms will now be selected.
	7. Press the <Del> key. This will delete all selected atoms together with the involved bonds.
	8. Click on the “Connectivity” button to open the “Connectivity” dialog. Increase the “DMax” value for the atom type combination “C - C” to 4 Å.
	9. Click on the “Connect” button to connect all  carbon atoms with each other. The resulting alpha-C-chain gains a good view on secondary structural elements such as alpha-helices.


Tutorial: Special Techniques: Surfaces with Defined Orientation
Special Techniques: Surfaces with Defined Orientation

For special applications, it is useful to examine plain parts of crystal structures with well-defined orientation. This is an easy task for DIAMOND and will be demonstrated with the alloy AgAuZn2 for example.

	Click on the “Open” button to open the File Open dialog, where you open the file “Alloy.dsf” from the “Samples\Tutorial” directory.
	Then click on the “Space-filling model” button to change to the space-filling model.
Filling a Rectangular Area

	1. Choose the “View” command from the “Display” menu to open the “View” dialog. Enter the values “1”, “1”, and “0” (in this order) into the input fields next to “u,v,w”, and then click on the “Set” button. (The coordinate system in the upper left corner of the structure picture will show you the new orientation.) Close the dialog.
	2. Click on the “Fill area” button. (The mouse symbol will change to an arrow with a dotted rectangle.) Now pull up a frame around a larger part of the structure window. After that, DIAMOND will calculate and display the dimensions in the “Fill cell range” dialog, where you can define the depth of the area to be filled in “ZMin” and “ZMax”. The z values refer to the origin of the unit cell. Choose ZMin=0 and ZMax=1 [Å].
	3. Choose the "Rotate" command from the "Display" menu. In the "Rotate structure" dialog, enter 90 degrees for the x- and zero for both y- and z-axis, then confirm with "OK".
	4. Push the "Add cell edges" button in the "Build" toolbar.
	5. Push the "Perspective" button in the "Display" toolbar to change to central projection. (For the previous filling of the cell area we needed parallel projection.)
	6. Use the Cursor keys to rotate the layer a little bit around the x- and y-axis of the view coordinate system to come to the following orientation:

The displayed plain consists of one layer of atoms only. Other values for „ZMin“ and „ZMax“ generate other layers, which may also be relevant.