MacroModel Quick Start Guide - ISP

Chapter 2: Using MaestroFigure 2.5. The Hydrogen Treatment panel.2. Enter 1err_htreat in the Entry name text box and click Create to update the ProjectTable with the new entry.2.8 Creating and Viewing SurfacesExamining the surface of a molecule frequently leads to valuable insights. Maestro can createseveral surface types. Surfaces can be rendered in different styles, color schemes, and transparency.Maestro surfaces are associated with project entries.This set of exercises uses the 1err.prj project from the previous section. If you are startingthe tutorial at this point, follow the instructions in Section 2.1, Section 2.2, Section 2.6, andSection 2.7 to set up the project for these exercises.2.8.1 Creating a Molecular Surface of a ComplexMaestro can create molecular surfaces that represent solvent-accessible regions of an entry.The molecular surface is a Connolly surface where a probe, typically with a radius of 1.4 Å, isrolled over the molecule. The surface is defined by the contact of the probe’s outer radius andthe molecule’s van der Waals radius.To generate a molecular surface for all atoms in the entry:1. Open the Project Table panel (Open/Close Project Table toolbar button).2. Click the In field for the 1err entry to include it in the Workspace.MacroModel 9.7 Quick Start Guide 15