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,
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.
Chapter 1: Maestro Overview
Maestro 10.2 User Manual
9
• 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
.