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Administrator Example: To examine the Deviation from Plane for five atoms in a penicillin molecule: 1. Build a penicillin model, as in the previous example. 2. Using the Select tool, click on the S (4) atom. 3. Shift+click the other atoms in the five-membered penicillin ring. The molecule should appear as follows: The result indicates that the atoms in the fivemembered ring of penicillin are not totally coplanar; there is a slight pucker to the ring. Removing Measurements from a Table You can remove information from the Measurements table without affecting the model. To remove measurements from a table: • From the Structure menu, point to Measurements and choose Clear. Displaying the Coordinates Tables You can view the internal coordinates or the Cartesian coordinates of your model by choosing Cartesian Table or Z-Matrix Table from the View menu. 4. From the Structure menu, choose Deviation from Plane. When the deviation from plane calculation is complete, the value appears in the Output window. Internal Coordinates The Internal Coordinates table contains one entry for each atom. The fields contain a description of how each atom in the model is positioned relative to the other atoms in the model. The order of atoms in the Internal Coordinates table is determined by the Z-matrix. The origin atom is listed first, and the rest of the atoms are listed in the order that they are positioned. For more information see “Scaling a Model” on page 79. 104•Inspecting Models CambridgeSoft Measurement Table
To display the Internal Coordinates table: 1. From the View menu choose Z-Matrix Table. The Internal Coordinates table appears. determined by their serial numbers. All of the atoms in a fragment are listed in consecutive records. Hydrogen, lone pair and dummy atoms are listed after heavy atoms. To display the Cartesian Coordinates table, do one of the following: • If the Tables window has been activated, click the XYZ tab at the bottom of the window. • If the Tables window has not been activated, choose Cartesian Table from the View menu. The Cartesian Coordinates table appears. The Cartesian Coordinates table acts like the other tables: you can select atoms or bonds either in the table or in the model. Use the pin icon to collapse the window to save space. Collapsed table tabs NOTE: The default condition is that all of the tables open in a tabbed window when you select any one. When you select a record in the Internal Coordinates table, the corresponding atom is selected in the model. When you select atoms in the model, the corresponding records are selected in the Internal Coordinates table. To edit measurements in the Z-matrix: 1. Type a new measurement in the selected cell. 2. Press the Enter key. To change which atoms Chem3D uses to position each atom use the commands in the Set Z-matrix submenu in the Structure menu. Cartesian Coordinates The fields in the Cartesian Coordinates table contain the atom name and the X-, Y- and Z- coordinates for each atom. The order of atoms is Mouse over a tab to display the table. The most recently used table displays the full name. Comparing Models by Overlay The Overlay submenu on the Structure menu is used to lay one fragment in a model window over a second fragment. Each fragment remains rigid during the overlay computation. Common uses of Overlay include: • Comparing structural similarities between models with different composition. • Comparing conformations of the same model. ChemOffice 2005/Chem3D Inspecting Models • 105 Comparing Models by Overlay
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Chapter 31: Changes and Audit Trail
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Administrator Tutorial 7: Docking M
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CHEMICAL Chemical Databases Referen
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CONSULTING & Consulting & Services
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CS Software Problem Report For fast
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