CS Chem3D(R) Version 4.0 For Windows 95 and Windows NT © 1986-1997 CambridgeSoft Corporation, All Rights Reserved. December 12, 1997 This Read Me file provides information not documented elsewhere about the Chem3D Pro application and known problems in the version 4.0 release. Additional information is available on the CambridgeSoft World Wide Web page (http://www.camsoft.com). ++++++++++New features in CS Chem3D version 4.0++++++++++++ * Links to CS MOPAC, now based on MOPAC 97 with MNDO-d (Chem3D Pro & Chem3D Ultra) * Links to Gaussian (Chem3D Ultra) * Extended Huckel Surfaces (Chem3D Pro & Chem3D Ultra) * Solvent Accessible Surfaces * Molecular Orbitals * Charge Density Surfaces * Spin Density Surfaces * Molecular Electrostatic Potential Surfaces * ChemDraw 4.0 (.cdx) File Format Support * Additional File Format Support * Improved Trackball Interface * Simplified Structure Cleanup ------------------------------- RELEASE NOTES Upgrading Windows: If you upgrade your Windows operating system, Chem3D must be reinstalled before further use. Users of Microsoft Plus! for Windows 95: Chem3D will be able to display models better if you turn off the Show window contents while dragging checkbox in the Plus! tab of your Display settings. Video/display drivers: to get the best display results from Chem3D, it is a good idea to use the most recent drivers for your video card. Contact the manufacturer of your video card for the most up-to-date drivers. You may find that memory is tight under some circumstances. Here are some steps you can take to reduce memory usage: * Reduce the number of model or table windows you have open. * Reduce the size of model windows. * Avoid displaying Space Filling models while building. * Do not record movie frames while doing minimizations or rotations. * If your model has more than one movie frame, use Edit/Clear Frames/Clear All Other Frames to eliminate unneeded frames. * If you have performed calculations, use Edit/Clear Calculations to eliminate unneeded calculations. * If you have created surfaces, use Edit/Clear Molecular Surfaces to eliminate unneeded surfaces. * In Movie Settings, reduce Smoothness (move the slider to the right) to decrease the number of frames saved while rotating. * Close Messages and Measurements windows when you no longer need them. * Close the Table Editor rather than leaving it in the background or minimized on the desktop. If you receive a warning that memory is low, please exit and restart Windows, then restart the program. Speed: Chem3D does a lot of work while you are building or minimizing a model. If you find the program to be slow during these operations, here are some steps you can take to increase speed: * Simplify the display. Use Wire Frame or Ball and Stick model types; choose Solid Colors instead of Shadowed. * If you have a Messages or Measurements window open, clear its contents: select the window, then choose Edit/Select All, Edit/Clear. * Close any windows you are not using. * If the Table Editor is running in the background, close any windows it has open; better yet, close the Table Editor and run Chem3D only. * If ChemDraw is running in the background, close it. CS MOPAC Std and MOPAC Pro: When this installer is run, specific information about the location of CS MOPAC is stored in your system. If you change the location of CS MOPAC, this information will no longer be correct and you will have to reinstall. Occasionally, the CS MOPAC application may terminate abnormally during a computation, leaving the model still waiting for results. If this happens, press the stop button. You can then try the computation again. OLE Automation: You must run Chem3D at least once before it will be available as an OLE Automation server. For the most up-to-date additional documentation on the OLE Automation interface, please see the Chem3D SDK information on your CD-ROM or visit our web site http://www.camsoft.com. ------------------------------- SUBSTRUCTURES If you wish to create your own substructures for the substructure table, use these settings to get your pictures to match those already present: Scale factor: 15/32 normal size Model Type: Ball and Stick Color by Element: On Color by Depth: On Atom Size: 16 Bond Width: 10 Depth Ratio: 75 ------------------------------- PARAMETERS If you wish to create your own parameters for use in model building or minimization, you can do so without altering the files provided. When Chem3D loads parameters to create its internal tables, it reads all files in the C3DTABLE directory and concatenates them together. Therefore, you can create your own separate parameter files, place them in the C3DTABLE directory, and have them automatically appended to the standard ones. For example, suppose you have a set of MM2 atom types which apply to a particular class of heterocycles. You can: (a) Create your own small table of these parameters, and use it as a supplement to the standard list. Using the Templates menu in the Table Editor, select MM2ATYPE.TBT to open a new, empty table. Use the Edit menu to create new records, and then fill in the data. Save the completed file in the C3DTABLE directory, for example with the name MYATYPES.TBL. Chem3D will then automatically use this table in addition to the standard MM2ATYPE.TBL. OR: (b) Modify the existing set of parameters to include your own. In the Table Editor, open MM2ATYPE.TBL, and use Save As to save a backup copy in a directory other than C3DTABLE. Edit the table as desired, modifying or deleting existing records and adding your own. Save the edited file in the C3DTABLE directory with whatever name you choose. Chem3D will use this table the next time it needs these parameters. If there are conflicts --- multiple definitions of the same parameter --- results are undefined. If you want to define your own value, be sure to delete any existing one. ------------------------------- KNOWN BUGS Colors: colors in model windows and some parameter tables may not be displayed correctly under some circumstances. If this happens, click in the title bar of the window, or resize the window slightly. Pattern printing: element patterns do not print correctly when you print ELEMENTS.TBL or a model with pattern-filled atoms. Highlighting of table lines: lines of text which contain tabs are not correctly highlighted in the Messages window. Multi-line text cells: there are some display problems with multi-line text items in REFS.TBL. ROSDAL strings: some structures are not correctly converted to or from ROSDAL string format. TECHNICAL SUPPORT ----------------- To report bugs or ask questions, please use one of the following addresses. E-mail is preferred. E-mail: Internet: support@camsoft.com WWW: http://www.camsoft.com CompuServe: 76070,615 America Online: CamSoft Post: Technical Support Staff CambridgeSoft Corporation 875 Massachusetts Ave. Cambridge, MA 02139 Fax: 1 617 491-7203 Last Edited: 12/12/97