Maestro User Manual



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Contents

Schrödinger Software Release 2015-2

xvi

14.12  Builder Preferences

.......................................................................................... 372

14.12.1  

Behavior ...................................................................................................... 372

14.12.2  

Geometry cleanup....................................................................................... 373



14.13  

Job Preferences

................................................................................................ 374

14.13.1  

Starting ....................................................................................................... 374

14.13.2  

Monitoring ................................................................................................... 375

14.13.3  

Incorporation ............................................................................................... 376

14.13.4  

Directory ..................................................................................................... 377



14.14  

Molecular Representation Preferences

......................................................... 379

14.14.1  

Atoms and Bonds........................................................................................ 379

14.14.2  

Ribbons....................................................................................................... 381



14.15  

SMARTS Generation Preferences

.................................................................. 383

Chapter 15: 

Scripting in Maestro



............................................................................. 385

15.1  

The Scripts Menu

................................................................................................ 385

15.1.1  

Installing Scripts and Macros ........................................................................ 385

15.1.2  

Managing Scripts .......................................................................................... 387



15.2  

Using Python and Python Scripts

.................................................................... 388



15.3  

Scripting and KNIME Workflows

...................................................................... 389



15.4  

Using Command Scripts

.................................................................................... 390

15.4.1  

Command History ......................................................................................... 391

15.4.2  

Building a Command Script .......................................................................... 391

15.4.3  

Saving a Command Script ............................................................................ 392

15.4.4  

Opening Existing Command Scripts ............................................................. 392

15.4.5  

Running and Stopping Scripts ...................................................................... 392

15.4.6  

Copying Commands as Python Commands ................................................. 393

15.4.7  

Customizations You Can Perform With a Script ............................................ 393



15.5  

Creating Command Aliases

............................................................................... 394



15.6  

Creating Macros

.................................................................................................. 395

15.6.1  

Named Macros.............................................................................................. 395

15.6.2  

Function Key Macros .................................................................................... 396




Contents

Maestro 10.2 User Manual

xvii

Chapter 16: 

Saving Workspace Images

............................................................. 399

16.1  

Saving Images to a File

...................................................................................... 399



16.2  

Copying Images to Other Applications

........................................................... 402

Chapter 17: 

Using Maestro with Other Applications



.................................. 403

17.1  

Canvas

................................................................................................................... 403



17.2  

KNIME

.................................................................................................................... 403



17.3  

PyMOL

................................................................................................................... 403



17.4  

ChemDraw and ISIS/Draw

.................................................................................. 405

Chapter 18: 

Help


................................................................................................................. 407

18.1  

The Help Menu

..................................................................................................... 407



18.2  

Maestro Help

........................................................................................................ 408



18.3  

Context-Sensitive Help

....................................................................................... 410



18.4  

Manuals

................................................................................................................. 411



18.5  

Tutorials

................................................................................................................ 412



18.6  

The Schrödinger Web Site

................................................................................. 413



18.7  

Technical Support

............................................................................................... 414

Appendix A: 

The Maestro File Format



................................................................. 417

A.1  

Basic File Description 

......................................................................................... 417



A.2  

Data Blocks 

........................................................................................................... 417



A.3  

Compressed Format 

............................................................................................ 419



A.4  

Data Item Names 

.................................................................................................. 419



A.5  

Example Maestro File 

.......................................................................................... 419




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