Maestro User Manual

Chapter 2: The Maestro Main Window

Maestro 10.2 User Manual

13

For a description of the options for the maestro command, run the command with the -h

option. The optional filename specifies a file to be imported into the project, in any format that

Maestro recognizes by its extension. 

2.1.4

Choosing a Profile

Much of the Maestro interface can be configured or customized, through the use of prefer-

ences, toolbar, menu, and mouse customization, installation of scripts, and use of macros and

shortcuts. These configuration and customization options are stored in your user profiles direc-

tory. See 

Chapter 13

 for more information on customization and the user profiles directory. 

To allow the use of more than one set of customizations, Maestro supports the concept of

profiles. A profile is a named collection of customizations and preferences that can be applied

when you start Maestro. The profiles are stored in the user profiles directory, each in its own

folder (subdirectory). Profile names are case-sensitive, and can include spaces and other non-

alphanumeric characters. The main standard profiles are provided in the distribution:

• Maestro—for general use of Maestro.

• BioLuminate—a customization for the BioLuminate product.

• MaterialsScience—a customization for the Materials Science suite.

• Elements—a simplified Maestro interface designed for medicinal chemistry.

Some other standard profiles are available that perform different customizations, to simulate

the behavior of Maestro 9.1, to simplify the interface for new users, and to emphasize small

molecule features. These profiles are very similar to the main Maestro profile, except that they

may have fewer menu items, or some rearrangements of the toolbars. There is no custom

online help for these profiles, as there is for the main standard profiles, so you may find that

documented features are not available in these profiles.

When you start Maestro without specifying a profile

1

, the 

Choose Profile

 dialog box opens by

default. In this dialog box you can choose the profile, by selecting it from the list. To start

Maestro with the chosen profile, click 

Start

 or press 

ENTER

, or double-click on the profile you

want to use.

1.

Starting Maestro with a particular profile can be done from the command line or by using the icon for the pro-

file. 

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Chapter 2: The Maestro Main Window

Schrödinger Software Release 2015-2 

14

Figure 2.1. The Choose Profile dialog box.

You can set the default profile by clicking in the 

Default

 column. If you bypass this dialog box

by clearing the 

Show this dialog at startup

 option, the default profile is used to start Maestro.

To return to displaying this dialog box, choose 

Maestro 

→

 Customize 

→

 Profiles

, and select

Show the Choose Profile dialog box at startup

 in the 

Customize Profiles

 panel. More informa-

tion on customizing profiles is given in 

Section 13.4 on page 323

.

All descriptions in this manual are given for the Maestro profile.

2.2

The Main Window

The Maestro main window is shown in 

Figure 2.2

. The following main window components

are always visible: 

• Title bar—displays the project name and the current working directory if the relevant

preference is set—see 

Section 14.1.4 on page 338

.

• Auto-Help bar—automatically displays context-sensitive help

• Main menu bar—provides access to panels

• Workspace—displays molecular structures and other 3D graphical objects, such as sur-

faces and Phase hypotheses. Information on a single project entry can also be displayed in

the top left corner—see 

Section 14.5.2 on page 358

. 

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Chapter 2: The Maestro Main Window

Maestro 10.2 User Manual

15

Figure 2.2. The Maestro main window, showing all window components.

The following main window components can be displayed or hidden by choosing the compo-

nent from the 

Window

 menu. Your choice of which main window components are displayed is

persistent between Maestro sessions.

• Toolbars—contain buttons for many common tasks. See 

Section 2.4 on page 17

 for an

overview of the toolbars and references to more detailed information.

• Status bar—displays information about a particular atom, about structures in the Work-

space, or about the contents of the Workspace and job status. See 

Section 2.5 on page 23

.

• Clipping planes window—displays a small, top view of the Workspace that shows the

clipping planes and viewing volume indicators. Hidden by default. See 

Section 4.6 on

page 72

.

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Chapter 2: The Maestro Main Window

Schrödinger Software Release 2015-2 

16

• Sequence viewer—shows sequences for proteins displayed in the Workspace. Hidden by

default. See 

Section 2.6 on page 25

.

• Command input area—provides a place to enter Maestro commands. Hidden by

default. Command completion is supported for the keyword (but not the options).

When a distinction between components in the main window and those in other panels is

needed, the term main is applied to the main window components (e.g., main menu bar).

The toolbars are dockable: they can be moved to any side of the Workspace or dragged out of

the Workspace entirely.

You can expand the Workspace to occupy the full screen, by pressing 

CTRL+=

 or choosing

Workspace 

→

 Full Screen

. All other components and panels are hidden. To return to the

previous display, press 

ESC

. 

The following sections describe some of these main window components in more detail.

2.3

The Menu Bar

The menus on the main menu bar provide access to panels, allow you to enter commands, and

control the appearance and contents of the Workspace. The main menus are as follows: 

•

Maestro

—change directories, check for software updates, set preferences, customize

menus, toolbars, and mouse actions, display main window components, set up command

aliases and macros, interact with PyMOL, and quit Maestro. 

•

Project

—display Project Table and annotation; create, open, close, copy, delete, save,

back up, restore, and merge projects; import and export structures. For more information

on projects, see 

Chapter 9

.

•

Edit

—undo actions, copy and paste structures or images, delete Workspace objects, select

atoms, find atoms, build and modify structures, and mark entries.

•

View

—change the view of the Workspace objects (rotate, translate, zoom, align) or the

view attributes (clipping, perspective, depth perception, fog), enter or exit stereo mode,

save or restore particular views, tile the Workspace. 

•

Workspace

—control the display of the contents of the Workspace, save Workspace

images and Workspace “scenes”. 

•

Tools

—group atoms; measure, align, superimpose, and minimize structures; assign struc-

tural features; and view and visualize data. 

•

Applications

—set up, submit, and monitor jobs for Schrödinger’s computational pro-

grams. Some products have a submenu from which you can choose a specific task. 

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