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