Chem3D Users Manual - CambridgeSoft

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• Select Parallel to rotate the right view further to the right. Administrator Using Hardware Stereo Graphic Enhancement Chem3D 9.0 provides stereo graphics rendering for hardware that has stereo OpenGL capabilities. There are now a variety of stereo graphics cards, stereo glasses, and 3D monitors that can be driven by Chem3D. Hardware enhancement is enabled from the OpenGL tab in the Chem3D Preferences dialog, which you can access from the File menu. Hardware Stereo 2. Select Render Stereo Pairs to display two views of the model next to each other. The right view is the same as the left view, rotated about the Y-axis. 3. Specify the Eye Separation (Stereo Offset) with the slider. This controls the amount of Y-axis rotation. 4. Specify the degree of separation by clicking the Separation arrows. About 5% of the width is a typical separation for stereo viewing. To select whether the views are cross-eyed or direct, do one of the following: • Select Reverse to rotate the right frame to the left. If your left eye focuses on the right-hand model and your right eye focuses on the left-hand model, the two stereo views can overlap. Any 3D window opened after this mode is enabled will utilize hardware graphics capabilities if they are available and enabled. NOTE: You must enable “stereo in OpenGL” in the display adapter properties control, as well as in Chem3D preferences, and select the correct mode for the glasses/monitor you are using. 62 •Displaying Models CambridgeSoft Structure Displays
You can use depth fading and perspective with hardware enhancement, but should not activate other stereo modes. TIP: The Eye Separation slider on the Stereo and Depth tab of the Model Settings dialog box can be used to control separation. You should select the Disabled radio button when using hardware stereo. Molecular Surface Displays Molecular Surface displays provide information about entire molecules, as opposed to the atom and bond information provided by Structure displays. Surfaces show information about a molecule’s physical and chemical properties. They display aspects of the external surface interface or electron distribution of a molecule. Unlike atom and bond data, Molecular Surface information applies to the entire molecule. Before any molecular surface can be displayed, the data necessary to describe the surface must be calculated using Extended Hückel or one of the methods available in CS MOPAC or Gaussian. Under MOPAC you must choose Molecular Surfaces as one of the properties to be calculated. There is one exception to the requirement that you must perform a calculation before a molecular surface can be displayed. Solvent Accessible surfaces are automatically calculated from parameters stored in the Chem3D parameters tables. Therefore, no additional calculations are needed, and the Solvent Accessible command on the Choose Surface submenu is always active. Extended Hückel Extended Hückel is a semi-empirical method that can be used to generate molecular surfaces rapidly for most molecular models. For this reason, a brief discussion of how to perform an Extended Hückel calculation is given here. For more information, see Appendix 8: “Computation Concepts”. To compute molecular surfaces using the Extended Hückel method: • From the Computations menu, point to Extended Hückel, and choose Calculate Surfaces. NOTE: Before doing an Extended Hückel calculation, Chem3D will delete all lone pairs and dummy atoms. You will see a message to this effect in the Output window. At this point, a calculation has been performed and the results of the calculation are stored with the model. To compute partial charges using the Extended Hückel method: ChemOffice 2005/Chem3D Displaying Models • 63 Molecular Surface Displays
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computer, except as provided below.
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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator A variety of other ba
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3. From the Calculations menu, poin
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Desktop Software Enterprise Solutio
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SOLUTIONS Enterprise Solutions APPL
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Desktop to Enterprise Solutions Che
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SOFTWARE E-Notebook Ultra Ultimate
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SOFTWARE ChemDraw Ultra Ultimate Dr
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SOFTWARE Chem3D Ultra Ultimate Mode
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SOFTWARE ChemFinder/Word • Search
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SOFTWARE The Merck Index • Encycl
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SOLUTIONS •Development and deploy
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SOLUTIONS •Adds chemical data typ
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MANAGEMENT •Custom organization o
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MANAGEMENT • Indexes chemical str
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DISCOVERY • Accessed through your
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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