MacroModel Quick Start Guide - ISP

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