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Administrator modes and color settings are easy to control at a fine-grained level. Properties of atoms and bonds are easy to access and change. The Model Explorer is designed as a hierarchical tree control that can be expanded/collapsed as necessary to view whatever part of the model you wish. Changes are applied in a bottom-up manner, so that changes to atoms and bonds override changes at the chain or fragment level. You can show/hide/highlight features at any level. Hidden or changed features are marked in the hierarchical tree with colored icons, so you can easily keep track of your edits. See “Working With the Model Explorer” on page 107 for more information. Model Coordinates Each of the atoms in your model occupies a position in space. In most modeling applications, there are two ways of representing the position of each atom: internal coordinates and Cartesian coordinates. Chem3D establishes internal and Cartesian coordinates as you build a model. Z-matrix Internal coordinates for a model are often referred to as a Z-matrix (although not strictly correct), and are the most commonly used coordinates for preparing a model for further computation. Changing a Z-matrix allows you to enter relations between atoms by specifying angles and lengths. You display the Z-Matrix table by selecting it from the View menu. You can edit the values within the table, or move atoms within the model and use the Set Z-matrix submenu of the Structure menu. You can copy and paste tables to text (.txt) files or Excel spreadsheets using the commands in the context (right-click) menu. Below is an example of the internal coordinates (Z-matrix) for ethane: Cartesian Coordinates Cartesian coordinates are also commonly accepted as input to other computation packages. They describe atomic position in terms of X-, Y-, and Z-coordinates relative to an arbitrary origin. Often, the origin corresponds to the first atom drawn. However, you can set the origin using commands in the Model Position submenu of the Structure menu. Instead of editing the coordinates directly in this table, you can save the model using the Cartesian Coordinates file format (.cc1 or .cc2), and then edit that file with a text editor. You can also copy and paste the table into a text file or Excel worksheet using the commands in the context (right-click) menu. NOTE: If you do edit coordinates in the table, remember to turn off Rectify and Apply Standard Measurements in the Model Build panel of the Model Settings dialog while you edit so that other atoms are not affected. An example of the Cartesian coordinates for ethane is shown below. 24 •Chem3D Basics <strong>CambridgeSoft</strong> Model Building Basics
The Measurements Table The Measurements table displays bond lengths, bond angles, dihedral angles, and ring closures. When you first open a Measurements Table, it will be blank. To display data in a Measurements Table: • From the Structure menu, point to Measurements, then select the information you wish to display. The example shows the display of Bond Lengths and Bond Angles for ethane: If you edit the Actual field, you change the value in the model, and see atoms in the model move. If you edit the Optimal value, you apply a constraint. These values are used only in Clean Up (on the Structure menu) and MM2 computations. Deleting Measurement Table Data You can isolate the information you in the Measurements table by deleting the records that you do not want to view. For example, you could display bond lengths, then delete everything except the carbon-carbon bonds. This would make them easier to compare. To delete records: • Select the records and click Delete on the rightclick menu. Deleting records in a Measurements table does not delete the corresponding atoms. To clear the entire table: • On the Measurement submenu of the Structure menu, select Clear. <strong>ChemOffice</strong> 2005/Chem3D Chem3D Basics • 25 Model Building Basics
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Page 12 and 13: A Guide to CambridgeSoft Manuals An
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Page 18 and 19: Administrator Connection Table . .
Page 20 and 21: Administrator Specifying Properties
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CONSULTING & Consulting & Services
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CS Software Problem Report For fast
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