Maestro User Manual



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Schrödinger Press

Maestro User Manual



Maestro 

10.2 

User Manual




Maestro User Manual Copyright © 2015 Schrödinger, LLC. All rights reserved. 

While care has been taken in the preparation of this publication, Schrödinger 

assumes no responsibility for errors or omissions, or for damages resulting from 

the use of the information contained herein.

Canvas, CombiGlide, ConfGen, Epik, Glide, Impact, Jaguar, Liaison, LigPrep, 

Maestro, Phase, Prime, PrimeX, QikProp, QikFit, QikSim, QSite, SiteMap, Strike, and 

WaterMap are trademarks of Schrödinger, LLC. Schrödinger, BioLuminate, and 

MacroModel are registered trademarks of Schrödinger, LLC. MCPRO is a trademark 

of William L. Jorgensen. DESMOND is a trademark of D. E. Shaw Research, LLC. 

Desmond is used with the permission of D. E. Shaw Research. All rights reserved. 

This publication may contain the trademarks of other companies.

Schrödinger software includes software and libraries provided by third parties. For 

details of the copyrights, and terms and conditions associated with such included 

third party software, use your browser to open third_party_legal.html, which is in 

the docs folder of your Schrödinger software installation.

This publication may refer to other third party software not included in or with 

Schrödinger software ("such other third party software"), and provide links to third 

party Web sites ("linked sites").  References to such other third party software or 

linked sites do not constitute an endorsement by Schrödinger, LLC or its affiliates.  

Use of such other third party software and linked sites may be subject to third 

party license agreements and fees. Schrödinger, LLC and its affiliates have no 

responsibility or liability, directly or indirectly, for such other third party software 

and linked sites, or for damage resulting from the use thereof.  Any warranties that 

we make regarding Schrödinger products and services do not apply to such other 

third party software or linked sites, or to the interaction between, or 

interoperability of, Schrödinger products and services and such other third party 

software.

May 2015



Maestro 10.2 User Manual

iii

Contents

Document Conventions



................................................................................................... xix

Chapter 1: 

Maestro Overview

........................................................................................ 1

1.1  

General Interface Design

......................................................................................... 1

1.1.1  

Maestro Windows ............................................................................................... 2



1.1.2  

Mouse Functions................................................................................................. 2

1.1.3  

Keyboard Shortcuts and Shortcut Menus ........................................................... 3



1.1.4  

File and Directory Selection ................................................................................ 3



1.2  

Maestro Workflow 

..................................................................................................... 5



1.3  

Maestro Projects

........................................................................................................ 6



1.4  

Access to Applications

............................................................................................ 7



1.5  

Running Jobs

............................................................................................................. 9



1.6  

Citing Maestro in Publications

.............................................................................. 10

Chapter 2: 

The Maestro Main Window



.................................................................. 11

2.1  

Starting Maestro

...................................................................................................... 11

2.1.1  

Starting Maestro on a Windows Host................................................................ 11



2.1.2  

Starting Maestro on a Mac Host ....................................................................... 12

2.1.3  

Starting Maestro on a Linux Host ..................................................................... 12



2.1.4  

Choosing a Profile............................................................................................. 13



2.2  

The Main Window

.................................................................................................... 14



2.3  

The Menu Bar

........................................................................................................... 16



2.4  

The Main Window Toolbars

................................................................................... 17

2.4.1  

The Project Toolbar ........................................................................................... 20



2.4.2  

The Edit Toolbar ................................................................................................ 21

2.4.3  

The Workspace Toolbar .................................................................................... 23



2.5  

The Status Bar

......................................................................................................... 23



2.6  

The Sequence Viewer

............................................................................................. 25



2.7  

Shortcut Menus

....................................................................................................... 26




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