MacroModel Quick Start Guide - ISP

Chapter 2: Using Maestro2.9.1 Defining an Atom Set by Selecting AtomsWith the contents of 1err_htreat.mae displayed in the Workspace, make a set that includesall atoms in the ligand:Set 1: Ligand1. From the Tools menu, choose SetsThe Sets panel opens.2. Click New (in the lower portion of the panel).3. Enter ligand in the Set name text box, and click OK.A new set is created, named ligand.4. In the Sets panel, under Atoms for set, select Show markers (see Figure 2.11).5. Choose Molecules from the Pick menu.6. In the Workspace, select an atom in the ligand to define the ligand set.If you need to identify the ligand, color the atoms by molecule number, or use the FindAtoms panel described on page 9. If you do use Find Atoms, deselect Mark found atomsonce you have selected the desired atom.Maestro highlights the atoms in the ligand set in green. Highlights are displayed as lines anddots, or as boxes, depending on the molecular representation of the atoms and bonds.Figure 2.11. The Sets panel.22MacroModel 9.7 Quick Start Guide