General Preferences

This section provides settings for storage of recently used items for later use.

Command history

These options can be used to limit the number of commands stored, and therefore available in the Command Script Editor panel.

• Unlimited—Store all commands.
• Limited—Store the number of commands given in the text box. When this limit is exceeded, the oldest commands are removed from the history.

Recently used list

In this text box, you can specify how many items are displayed on the lists of recently used projects and recently imported files, which are displayed with File → Open Recent Project and File → Import Recent Structures.

These settings determine some of the directories that are used by Maestro.

Default directory for job startup and file i/o options

When you choose any of the options below, the current working directory is set to the specified location, and the option you select is stored as a preference. The current working directory is set to the specified location the next time you start Maestro.

Job files are written by default to the current working directory. File selectors display the contents of the current working directory when they are first opened in a Maestro session. Subsequently each file selector stores the last location you visted, and displays the files in that location when you open it again.

Thus, these options set the default by changing the current working directory immediately, on Maestro startup, and when a project is opened if the option is project-related.

If you change the current working directory explicitly after choosing one of these options, the new directory is used as the location for job files and the initial location for file selectors, rather than the choice you make from this set of options. For more information on changing the current working directory, see Changing the Working Directory.

In the descriptions below, the directory is called the default directory.

Note: If you choose an option for a directory that is inside the project, you should wait until any jobs launched from that project finish before you rename the project, or save the project if it is a scratch project.

• Maestro's current working directory—Set the current directory to Maestro's initial working directory. When Maestro starts, this directory on Linux is the directory from which Maestro was started; on Windows and Mac it is the Schrodinger folder in your Documents folder.

• Parent of project directory—Set the current working directory to the parent directory of the current project (the directory that the project is in). Opening a different project or closing a project (which opens a scratch project) sets the current working directory again. For zipped projects, the parent directory is the directory that contains the .prjzip file, rather than the temporary directory into which the zipped project is extracted. This is the default setting for the Materials Science profile.

  Jobs running with this setting are not lost if the project is renamed.

• Project directory—Set the current working directory to the top-level directory inside the current project. This is the project-name.prj directory. This directory changes when a new project is loaded, and the current working directory is reset to the new project directory.

  Jobs running in this directory will fail if the project is renamed. This includes saving scratch projects.

• Project jobs directory—Set the current working directory to the project's jobs subdirectory (project-name.prj/jobs). This directory changes when a new project is loaded or when a scratch project is opened, and the current working directory is reset to the new jobs directory.

  Jobs running in this directory will fail if the project is renamed. This includes saving scratch projects.

• Other (specify below)—Use the specified directory as the current working directory. When using this option, you must enter the desired directory name in the Directory text box.

Custom directory for file i/o options

Specify the location of the custom directory to use in file selectors. The contents of this directory are displayed when you click the Custom icon in a file selector under Look in. There are two standard locations that you can select as the custom location, or you can choose your own location.

• Maestro installation directory—Set the custom directory to the directory in the installation that contains the Maestro software and resources. The actual path is displayed in the tooltip for this option.

• Maestro launch directory—Set the custom directory to the directory from which Maestro was started, on Linux, or the Schrodinger folder in your documents folder on Windows and Mac. The actual path is displayed in the tooltip for this option.

• Other (specify below)—Specify the directory in the Directory text box.

File chooser dialogs (Windows only) options

Set options for the use of native Windows file choosers when there are options associated with reading or writing files. The use of a custom file chooser can be slow at times.

• Avoid custom file dialogs—When possible, use the native Windows file dialog box, and present the options for the action in a separate dialog box. This option is selected by default. If this option is not selected, the custom file chooser with the options included is used.

• Skip confirmations - always use defaults—Once the files have been chosen in the Windows native file chooser, read or write the files immediately with the last settings used. If this option is not selected, a second dialog box opens after the selector, to make settings for the file operations.

These settings control Maestro's default file suffix for several different file formats. A default suffix is automatically appended to a file name if that file name has no suffix. The default file suffixes are:

• Maestro — mae
• Maestro compressed — maegz
• PDB — pdb
• Mol2 — mol2
• SD — sdf
• SD compressed — sdfgz

These settings control the appearance or layout of Maestro.

Show tooltips option

When the pointer is paused over a control, show information about the control in a box near the control after a short delay. The box is hidden after a period of time, or when the pointer is moved. This information in a box is known as a tooltip or balloon help.

Main title bar information options

Show the selected information in the title bar of the main window, in addition to the application name and suite (Maestro, Maestro BioLuminate, etc.) and the project name. The options are:

• Maestro version number
• Current working directory
• Full project path

The order in which the information is shown is version number, project path, directory. The full project path replaces the project name.

Set the font, size, and style for the text. The Regular settings control the fonts in all the application panels: headings, button labels, menu items, and so on. The Text editing settings control the fonts in all places where you can edit text (text boxes, tables, and so on). The Project Table settings control the fonts for the text that is displayed in the column headings and the table cells in the Project Table. The Toolbar buttons settings control the fonts for the text that is displayed on toolbar buttons.

An example of the font size is given under each option menu. You must restart Maestro to apply the new fonts.

Control the docking, location, and choice of panels.

Allow docking of panels option

This option allows panels to be docked into the Workspace. Most of the panels other than those on the Applications or Tasks menu are dockable. This option is selected by default. If it is not selected, when you open these panels, they are opened outside the Workspace and cannot be attached to the Workspace (docked).

Location options

Specify the location to place the docked panels. They can be docked in either the main window, or in a floating window, named Docked Panels.

Show dialog boxes at the position of the pointer

When a dialog box opens, center it on the current pointer position. If you turn this option off, the dialog box is displayed at its last displayed location (or its default location if it has not been displayed).

Always show panels on top of main window

Show all panels in front of the main window, and ensure that they do not go behind the main window.

Select the information that is shown or saved when Maestro quits.

Warn when quitting Maestro option

Display the Quit panel when quitting Maestro, which provides an opportunity to cancel the quit operation.

Save panel layout option

Save the panel layout (size, location) of all panels that have been opened in a Maestro session in a resource file when Maestro quits. The layout is read the next time Maestro is started. You can also save the layout by choosing Window → Save Layout.

Write command log file option and text box

Write a log of commands used in the Maestro session to the log file specified in the text box. The log file is written to Maestro's working directory. This information can be useful to Schrödinger support staff when responding to any problem you report.