MacroModel Quick Start Guide - ISP

Chapter 2: Using MaestroFigure 2.9. The Proximity dialog box.5. In the Molecule tab, select Molecule Number from the list on the left and enter 4 in theMolecule Number text box.6. Click Add.7. Click Proximity.The Proximity dialog box opens (see Figure 2.9).8. Under Proximity, select Within and Angstroms, and enter 5.0 in the text box.9. Under Fill, select Residues and select Exclude source.10. Click OK in the Proximity dialog box and in the Atom Selection dialog box.11. In the Molecular Surface panel, under Surface context, select Molecule. Click Create Surface.The resulting surface clearly defines the topology of the binding site.12. Close the Molecular Surface panel.In the Manage Surfaces panel, you can click Display Options and color the surface bypartial charge or residue charge to visualize the electrostatics topology. You can alsochange the style or transparency to see the atoms under the surface. When you are finished,close the Display Options panel and the Manage Surfaces panel.13. Choose Surface > Undisplay All from the Display menu.2.8.4 Creating a Map of the Binding SiteMaestro can be used to create “maps” of receptors. The map shows hydrophobic and hydrophilicregions, and is a tremendous asset when manually docking or adjusting ligands in areceptor. For this exercise, use the structure that was given the hydrogen treatment and map theMacroModel 9.7 Quick Start Guide 19