Maestro

• Documentation as PDF files in the directory: /usr/glea/schrodinger/docs/maestro5/pdf/

This command creates a window, most of which is the black area of the Workspace, with menus along the top, and other options to the right.

Maestro organises molecules into projects. The first thing to do is to select a project, either by making a new one (Menu: Project->New Project...) or by opening an existing one (Menu: Project->Open Project...). This will create a Project Table which can be used to keep track of a list of molecules, each of which is an entry in the project. The Project Table does not save the structures - if a molecule appears in the Project Table it is possible that the files describing the molecule have already been deleted. Usually you will do a calculation on a molecule after building it, and this will save the structure as a file.

Molecules are imported into Maestro either by importing them from a file (Menu: Project->Import Structure...) or by building them from scratch (Menu: Project->Build...). Both these options creates a new panel, with a variety of options: the first for selecting files of molecules, and controlling how many molecules are imported from it; the second with a wide range of options for drawing molecules.

A molecule in the Workspace can be rotated by holding down the middle mouse button (or mouse wheel) and moving the mouse. They can be translated or re-centred using the right-hand mouse button. They can be zoomed by pressing the middle and right buttons together.

Molecules which are imported from files are automatically added to the Project Table. The third column of this contains checkboxes, which can be selected to decide which molecules from the project will be shown on the Workspace. In the picture below the Project Table lists cyclohexane, propane and an alanine alpha-helix, the last of which is selected in the third column of the table, and so displayed in the Workspace.

Molecules which are built in the Workspace are not put in the Project Table unless the computer is asked to do this (Menu: Project->Create Entry from Workspace...). This does not record the structure. To do this, you should either do a calculation on the structure, or else (Menu: Project->Export...) the structure to a file.

Quitting from Maestro (Menu: Maestro->Quit...; You have the option of saving the log file of the session, but the default is to delete it) loses the molecules in the Workspace. You can keep them for another session by exporting them to a file (Menu: Project->Export...). However, molecules are usually drawn so that calculations can be done on them, and both MacroModel and Jaguar will automatically create files to keep track of the calculations underway.

Once a molecule has been drawn, choose either MacroModel or Jaguar from the menu Applications. These will enable you to do calculations on the molecule.