标题: [转移贴]Intro to Pymol [打印本页] 作者: hantavirus 时间: 2015-6-8 13:51 标题: [转移贴]Intro to Pymol 原贴由donggua发表于 2011-11-27 06:57
Description
对于非营利用户和教育用户有免费版本的，需要注册。强烈建议这个软件。
PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone!
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
PYMOL userman A.pdf
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