Maestro User Manual

Chapter 1: Maestro Overview

Maestro 10.2 User Manual

7

Entries are represented by rows in the Project Table. Each row contains the row number; the

entry’s Workspace inclusion state (the 

In

 column); the title; a set of buttons (in the 

Title

column) to open panels if there is auxiliary data associated with the entry such as surfaces,

trajectories, vibrations, hypotheses; the entry ID, and any properties associated with the entry. 

You control which entries are displayed in the Workspace from the Project Table. You can use

entries as input for most of the computational programs. You can select entries as input for the

ePlayer, which displays the selected structures in sequence. You can duplicate, combine,

rename, split, and sort entries; create properties for entries, import structures as entries, and

export entries in various formats. Although the Project Table does not have spreadsheet capa-

bilities, you can export properties to and import properties from a spreadsheet. 

When you draw molecules in the Workspace, they constitute a scratch entry until you choose

to save the structures as project entries. The scratch entry is not saved with the project unless

you explicitly add it to the project. However, you can use a scratch entry as input for some jobs,

and the results can be incorporated.

For products that have wizard-based interfaces (CombiGlide, Phase, and Prime), data is stored

inside the project, grouped as entities called “runs”. Output from each step is incorporated into

the next step and stored in the project, but not via the Project Table. The data in the runs can

include structural data, but do not make use of the Project Table directly. Instead, structures can

be copied to and from the Project Table at various points in the run. 

More information on projects is given in 

Chapter 9

.

1.4

Access to Applications

Maestro provides panels for preparing and running jobs for most of Schrödinger’s applications.

Access to these applications are presented on the menu bar as two alternative menus, and also

in a panel that provides extra features for finding and selecting applications. The menus are:

•

Tasks

 menu—This menu lists the main tasks that can be performed by Schrödinger appli-

cations. If you know what kind of task you want to perform, you can use this menu. It is

displayed by default on the menu bar in the main window. If the 

Applications

 menu is dis-

played, choose 

Task View

 from this menu to display the 

Tasks

 menu.

•

Applications

 menu—This menu lists the available applications (products). If you are

familiar with the products, you can use this menu to find the panel you want to use. To

display this menu, choose 

Application View

 from the 

Tasks

 menu. 

Both of these menus are also displayed in tree form with search capabilities, in the 

Task Tree

and 

Application Tree

 panels. Like the menus, these panels are interchangeable and can be

switched from the panel itself. The 

Task Tree

 panel opens by default when Maestro is started,

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Chapter 1: Maestro Overview

Schrödinger Software Release 2015-2 

8

but you can open it by choosing 

Show Tree

 from either of the menus. A brief description of

how to use the panel is given in the lower section of the panel when it first opens. 

Figure 1.2. The Application Tree and Task Tree panels.

• To expand or collapse a submenu (node) in the tree, click on the + or – button. 

You can also expand and collapse the submenu by right-clicking on the name and choos-

ing 

Selected

 from the 

Expand

 or 

Collapse

 submenu, or expand a submenu and collapse

all others by choosing 

Expand

 

→ 

Only Selected

. 

• To expand or collapse all submenus, right-click on any submenu and choose 

All

 from the

Expand

 or 

Collapse

 submenu, or click the 

Settings

 button and choose 

Expand All

 or 

Col-

lapse All

.

• To display a description of a task or panel (leaf) in the lower section of the panel, click on

the task or panel.

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Chapter 1: Maestro Overview

Maestro 10.2 User Manual

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• To find a task or panel by searching the text of the menu, the name of the task or panel, or

its description, enter text in the search box at the top of the panel. Only the items that con-

tain matching text are shown in the tree. The tree is updated as you type. Click the clear

(X) button in the search box to clear the search text and redisplay the full tree.

• To open a panel, double click the task or panel name, or right-click on it and choose

Open

. 

In addition to the 

Tasks

 and 

Applications

 menus, the panel shows the 

Tools

 menu and the

Scripts

 menu. This allows you to search more widely for the task that you are interested in.

Maestro has a large number of application panels. If your workflow only uses a few of them, or

only uses a few of them most of the time, you can designate “favorite” applications, and

display a tree that only contains the favorites. To mark an item as a favorite, right-click on it

and select 

Favorite

. To show only the favorites in the tree, select 

Show Favorites Only

 on the

Settings

 button menu. The panel title is updated to reflect this choice. You can also restrict the

Tasks

 and 

Applications

 menus to only the designated favorites by selecting 

Show Favorites

Only

 on the menu. To show the full tree or menu, deselect this item.

The menus can also be customized—see 

Section 13.2 on page 318

.

1.5

Running Jobs

When you have set the appropriate options in an applications panel, you use the 

Job

 toolbar to

start the job. This toolbar is described in all the application manuals. Briefly, you can click 

Run

to run a job with the current job settings, or click the 

Settings

 button to open the 

Job Settings

dialog box and set options for running the job. See 

Section 2.2

 of the Job Control Guide for a

detailed description of the options in the 

Job Settings 

dialog box. When you have finished,

click 

Run 

to launch the job (and optionally open the 

Monitor

 panel), or click save to save the

settings for the next job. Note that most jobs that are run locally are automatically run at low

priority so that they do not significantly affect the performance of Maestro. Exceptions are

noted in this manual.

Maestro’s job launching and incorporation capabilities are designed to make it easy to manage

multiple structures and their passage though multiple computational programs, without having

to deal with the details of the file system. The running of jobs is handled by the Job Control

facility, which is described in detail in the 

Job Control Guide

. 

Input files for the job are written to the launch directory, which is Maestro’s 

current working

directory

. This directory can be changed by choosing 

Project 

→

 Change Directory

 and navi-

gating to the new directory in the 

Change Directory

 dialog box, or by entering the command cd

path in the 

Commands

 text box (command input area) in the main window. You can also set

preferences for this directory—see 

Section 14.1.2 on page 336

.

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