MacroModel Quick Start Guide - ISP

Chapter 2: Using Maestro4. Click Apply to see the changes.Figure 2.8. The Limit panel.The surface is limited to the part that is generated for molecule number 1.5. Click Select to open the Atom Selection dialog box.6. In the Molecule tab, choose Molecule Number from the list and enter 2 in the MoleculeNumber text box.7. Click Add, then click OK.8. In the Limit panel, click OK.The surface is extended to include molecule number 2.9. In the Manage Surfaces panel, deselect the Limit box for MolSurf1 to remove the surfacelimit and redisplay the entire surface.2.8.3 Generating a Surface for One Molecule in a ComplexAn entry can be composed of multiple molecules, such as a co-crystallized receptor-ligandcomplex. Maestro is capable of generating a surface using a subset of atoms in the entry. In thisexample, you will use the 1err entry to create a surface of just the atoms near the binding site,ignoring the ligand.1. Choose Surface > Molecular Surface from the Display menu.2. Enter MolSurf2 in the Name text box.3. Under Atoms for surface display, click the Clear button to clear the ASL text box.4. Click Select to open the Atom Selection dialog box.18MacroModel 9.7 Quick Start Guide