MacroModel Quick Start Guide - ISP

Chapter 2: Using Maestro2.9.2 Defining an Atom Set with the Atom Selection Dialog BoxThis exercise uses the Atom Selection dialog box to define more complex sets of atoms.Set 2: Glycine residuesCreate a set that contains all glycine residues in the structure:1. Create a new set named glycine.2. In the Sets panel, select Show markers.3. Under Atoms for set, click Select.The Atom Selection dialog box opens.4. In the Residue tab, select Residue Type from the list on the left, then select GLY from theResidue Type list in the center.5. Click Add, then click OK.You can switch between sets by selecting a set from the list at the top of the Sets panel.Set 3: All residues with atoms within 5 Å of the ligandCreate a set containing the ligand and all atoms in complete residues within 5.0 Å of theligand:1. Create a new set named lig+5A.2. In the Sets panel, under Atoms for set, click Select.The Atom Selection dialog box opens.3. In the Set tab, select User-defined from the list on the left, then select ligand from theUser-defined list in the center, and click Add.4. Click the Proximity button.The Proximity dialog box opens.5. Under Proximity, select Within and Angstroms, and enter 5.0 in the text box.6. Under Fill, select Residues.7. Click OK in the Proximity dialog box and in the Atom Selection dialog box.The lig+5A set is defined.MacroModel 9.7 Quick Start Guide 23