MacroModel Quick Start Guide - ISP

Chapter 2: Using Maestro2.2 Identifying, Labeling, and Deleting StructureElementsThis exercise demonstrates how to use Maestro’s display tools to inspect the protein-ligandcomplex and delete parts of the structure that are not needed for a calculation.The protein-ligand complex imported in the last exercise was obtained from the Protein DataBank repository. The structure contains crystallographic water molecules, which need to beremoved. Also, the structure is dimeric, and for most purposes only the monomer is required.To label the water molecules with the PDB name:1. In the Workspace, right-click on an atom in one of the outlying water molecules to spotcenteron the atom.2. Zoom in on the water molecules by scrolling with the mouse wheel or by dragging withthe middle and right mouse buttons, until you have a good view of the water molecules.3. Choose Composition from the Label picked atoms button menu.The Atom Labels panel opens (see Figure 2.2)4. Choose Molecules from the Label atoms pick menu.5. In the Composition tab, select Residue name and clear all other selections.6. In the Workspace, select one of the outlying water molecules of the structure to display itslabel: HOH.7. Close the Atom Labels panel.To delete unwanted atoms:1. Choose Waters from the Delete button menu.All the water molecules are deleted.2. Click the Fit to screen button.The entire protein is now visible.MacroModel 9.7 Quick Start Guide 7