MacroModel Quick Start Guide - ISP

Chapter 2: Using Maestro10. Click OK in the Proximity dialog box and in the Atom Selection dialog box.11. In the Hydrophobic/philic Surfaces panel, under Bounding box, choose Molecules from thePick menu and select an atom in the ligand.12. Enter 6.0 in the Box margin text box and choose Standard from the Grid Spacing optionmenu.13. Click Start to open the Start Job dialog box.The Start dialog box opens. You can keep the default settings.14. Click Start to start the job.15. Enter sitemap1SHD in the Name text box.16. Click Start to launch the job.When the job finishes, the surface is displayed in the Workspace and the Manage Surfacespanel opens.17. Close the Monitor panel.18. In the Manage Surfaces panel, experiment with the transparency and the isovalue. Forexample, select the philic surface in the table and enter -15.0 in the Isovalue text boxat the bottom of the panel. Enter -0.3 for the phobic isovalue.19. When you have finished, close the Manage Surfaces panel and the Hydrophobic/philicSurfaces panel.2.9 Creating and Manipulating Atom SetsDefining subsets of atoms can be useful for many analysis and visualization tasks as well as forpreparing MacroModel calculations. The Sets panel allows you to create and manipulate setsusing the full range of atom selection tools. Once created, sets can be used in the Atom Selectiondialog box or from relevant Pick menus. Sets are saved within a Maestro project. To usedefined sets in another project, you can write them to a file using the Write button, then readthem into the new project using the Read button.These exercises use the all-atom protein-ligand complex in 1err.mae:1. Choose New from the Project menu and name the project 1errsets.2. Import the structure from 1err_htreat.mae.See Section 2.1 on page 5 for instructions on importing a structure.MacroModel 9.7 Quick Start Guide 21