MacroModel Quick Start Guide - ISP

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Chapter 2: Using MaestroFigure 2.6. The Molecular Surface panel.3. Choose Molecular Surface from the Display > Surface in the main window.The Molecular Surface panel opens (see Figure 2.6).4. Enter MolSurf1 in the Name text box.5. Under Atoms for surface display, choose Entries from the Pick menu.6. Select Entry under Surface Context.The surface context describes the atoms for which the surface is created. The surface displaydescribes the atoms for which the resulting surface is displayed. You can change theatoms for which the surface is displayed after surface generation by using the Limit feature,which you will do in the next exercise.7. In the Workspace, select any atom in the entry.8. Click Create Surface.When the surface generation is complete, the surface is displayed in the Workspace andthe Manage Surfaces panel is displayed (see Figure 2.7).16MacroModel 9.7 Quick Start Guide
Chapter 2: Using MaestroFigure 2.7. The Manage Surfaces panel.You can experiment with the surfaces by doing any of the following:• Generate the same surface with High image quality (give it a different name).This calculation takes longer to generate, but the resulting surface has superior quality.Also, the resulting high quality surface may be slower to rotate depending on your workstationresources.• In the Manage Surfaces panel, click Display Options and experiment with different stylesand color schemes.The Partial Charge color scheme uses white until a calculation is performed. The structurewas imported from a PDB record, which has no information about the fractionalatomic charges. Therefore, these must be calculated before Maestro can render the partialcharge values on the surface. To use the partial charges from the OPLS_2005 force field,you can choose Assign Partial Charges from the Tools menu.2.8.2 Limits to a SurfaceFrequently the entire surface of an entry is not required. Instead of creating another surfacewith a smaller subset of atoms, you can display a portion of a generated surface using the Limitpanel. This exercise demonstrates how to limit the surface generated in the previous exercisefrom the entire entry to a smaller section of the entry.1. In the table, click the V field of the MolSurf1 entry to display it.2. Click Limit (in the lower portion of the Manage Surfaces panel) to open the Limit panel.3. Enter mol.num 1 in the ASL text box.MacroModel 9.7 Quick Start Guide 17
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