pymol 的使用手册

pymol 的使用手册

Copyright Notice and Usage Terms...................1
Copyright Notice..1
Terms of Usage for the PyMOL User's Manual............1
Trademarks..........1
Preface..............................2
Why PyMOL?......2
Words of Caution.2
Strengths..............3
Weaknesses..........3
Introduction.....................4
Welcome to PyMOL!................................4
Is PyMOL Free Software?........................4
Yes, but..........4
The DeLano Scientific Mission................4
Installation.......................6
Windows..............6
Recommendations..............................6
Minimal System Requirements..........6
Python-Free Installation....................6
Python-Dependent Installation..........6
MacOS X.............6
Recommendations..............................7
Minimial Requirements......................7
If you use Fink....................................7
If you do not use Fink.........................7
Linux and Unix....8
System Requirements.........................8
Dependency-Free Approaches..........8
Dependency-Based Approaches........9
Getting Started with Mouse Controls..............10
Launching..........10
Using the Mouse...............................10
Using a Command Line....................10
PyMOL's Windows.................................11
The Viewer Window........................11
The External GUI Window..............12
Loading PDB Files..................................13
Manipulating the View...........................13
Basic Mouse Control........................13
Virtual Trackball Rotation................14
Moving Clipping Planes...................16
Changing the Origin of Rotation......16
Getting Comfortable.........................17
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Table of Contents
Getting Started with Commands......................18
Recording Your Work (Optional)...........18
Loading Data......18
Manipulating Objects..............................19
Atom Selections...............................19
Coloring Objects and Selections......21
Turning Objects and Selections On and Off.........22
Changing Your Point of View...............23
Saving Your Work..................................23
Scripts and Log Files........................24
png Files......24
Session Files.....................................25
Command-Line Shortcuts......................25
Command Completion using TAB...26
Filename Completion using TAB.....26
Automatic Inferences.......................26
Other Typed Commands and Help........27
Command Syntax and Atom Selections...........28
Syntax................28
Selection-expressions......................28
Named Atom Selections...................29
Single-word Selectors......................31
Property Selectors.............................31
Selection Algebra.............................34
Atom Selection Macros....................35
Calling Python from within PyMOL......37
Cartoon Representations...................................38
Background........38
Accessibility.....................................38
Pretty and Correct.............................38
Customization....41
Cartoon Types..................................41
Fancy Helices...................................44
Secondary Structure Assignment............45
Ray-Tracing..................46
Important Settings...................................46
Saving Images....47
png...............47
Stereo..............................48
Introduction........48
Supported Stereo Modes.........................48
Crosseye Stereo................................48
Walleye Stereo.................................48
Hardware Stereo...............................48
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Table of Contents
Stereo
Generating Stereo Figures.......................48
Movies............................49
Concepts.............49
States and Frames.............................49
Important Commands To Know.............49
load..............49
mset.............49
mdo..............50
mmatrix.......50
Simple Examples....................................50
Complex Examples.................................51
Previewing Ray-traced Movie Images...51
cache_frames....................................51
mclear..........51
Saving movies....51
mpng............52
Advanced Mouse Controls................................53
Picking Atoms and Bonds.......................53
Example Usage of the "pk" Atom Selections..............53
The "lb" and "rb" Selections...................53
Conformational Editing..........................54
Crystallography Applications...........................55
Crystal Symmetry...................................55
load..............55
symexp.........55
Electron Density Maps............................56
load..............56
isomesh and isodot...........................56
Compiled Graphics Objects (CGOs) and Molscript Ribbons.................................57
Introduction........57
Molscript Ribbons...................................57
load..............57
Using Molscript................................57
Creating Compiled Graphics Objects.....58
CGO Reference..59
load_cgo......59
Callback Objects and PyOpenGL....................61
Introduction........61
Example.............61
load_callback....................................62