Difference between revisions of "Main Page"

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## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
 
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
 
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
 
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
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# [[Using the GUI]]
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# [[:Category:Using Pymol|Using PyMol]]
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## [[Mouse Controls]]
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## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
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## [[Objects and Selections]]
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## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
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### [[Working with Objects]]
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### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
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### [[Working with Selections]]
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### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
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### [[Selector Quick Reference]]
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### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
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#### [[Single-word Selectors]]
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#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
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#### [[Property Selectors]]
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#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
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#### [[Selection Algebra]]
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#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]
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#### [[Selection Macros]]
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#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]
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### [[Representations]]
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### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
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#### [[Lines]]
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#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
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#### [[Sticks]]
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#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
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#### [[Cartoon]]
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#### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]
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#### [[Surface]]
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#### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]
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#### [[Mesh]]
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#### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]
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#### [[Spheres]]
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#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
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#### [[Dots]]
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#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
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### [[Color]]
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### [[:Category:Using Pymol Objects and Selections Color|Color]]
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### [[Displaying biochemical properties]]
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### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
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## [[Display Settings]]
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## [[:Category:Using Pymol Display Settings|Display Settings]]
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## [[Stereo 3D Display]]
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## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
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### [[Hardware Options]]
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### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
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### [[Linux XFree86 Configuration]]
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### [[Linux XFree86 Configuration]] -- wrong place
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## [[Scenes]]
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## [[:Category:Using Pymol Scenes|Scenes]]
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## [[Mouse Settings]]
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## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
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## [[Wizards]]
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## [[:Category:Using Pymol Wizards|Wizards]]
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## [[Plugins]]
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## [[:Category:Using Pymol Plugins |Plugins]] -- wrong place?
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## [[Ray-tracing]]
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## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]
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## [[Settings Reference (all settings and what they do)]]
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## [[:Category:Using Pymol Settings Reference|Settings Reference (all settings and what they do)]]
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## [[Movies and Animations]]
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## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]
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## [[Structure Alignment]]
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## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]
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## [[Structure Alignment Editor]]
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## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]
 
# [[:Category:Commands|Command Language]]
 
# [[:Category:Commands|Command Language]]
 
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
 
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]

Revision as of 23:21, 17 February 2005

PyMol Wiki Home

You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.

Helping

If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages. We now need people to assist with

  • A wiki edit/user policy is needed.
  • Wiki schema/design/organization: Below you'll find the current layout design
  • Graphic design and CSS layout: We need logos, BG images and CSS layout
  • Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
  • Etc...

Editors Needed

If you feel you have the time to help import data into the PyMol wiki, please email Tree.

We need your help. So join today & happy editing!

Tree

Section Layout

Please do not ADD any content to the site yet. Just Organize the following list as logically as possible. Here's my first go at it.

Please see Discussion for more thoughts on the site organizaiton.

Layout Schema

  1. News
    1. Discussion
    2. PyMol Beta
  2. Technical Issues
    1. Installation
      1. OS Dependent
        1. Linux
        2. MAC
        3. Windows
  3. Launching PyMOL
    1. Command Line Options
    2. Launching From a Script
  4. Using PyMol
    1. Mouse Controls
    2. Objects and Selections
      1. Working with Objects
      2. Working with Selections
      3. Selector Quick Reference
        1. Single-word Selectors
        2. Property Selectors
        3. Selection Algebra
        4. Selection Macros
      4. Representations
        1. Lines
        2. Sticks
        3. Cartoon
        4. Surface
        5. Mesh
        6. Spheres
        7. Dots
      5. Color
      6. Displaying biochemical properties
    3. Display Settings
    4. Stereo 3D Display -- wrong place
      1. Hardware Options -- wrong place?
      2. Linux XFree86 Configuration -- wrong place
    5. Scenes
    6. Mouse Settings
    7. Wizards
    8. Plugins -- wrong place?
    9. Ray-tracing
    10. Settings Reference (all settings and what they do)
    11. Movies and Animations
    12. Structure Alignment
    13. Structure Alignment Editor
  5. Command Language
    1. PyMOL Command Script
    2. PyMOL Python API
  6. Advanced Issues
    1. Modeling and editing structures
      1. Editing Atoms
      2. Molecular sculpting
      3. Homology modeling
    2. Image Manipulation
      1. labels
      2. Photoshop/GIMP
      3. Stereo Figures
      4. Publication-quality images
  7. Scripting
    1. Example Scripts
    2. Script Library
  8. Plugins
    1. How to do electrostatics and energy minimization.
      1. APBS Plugin
    2. rtools
    3. Tutorial on writing plugins
    4. Others
  9. High-Level Applications (Crystallography, NMR)
    1. Crystallography Applications
      1. Symmetry
      2. Electron Density
    2. NMR Applications
      1. Working with Structure Families
      2. Superimposition and RMSD
      3. NMR Restraints and Analysis
  10. Third Party Software
    1. Movies
    2. Codecs
  11. Python Integration
  12. Unintended Uses (OpenGL Object Renderer)
    1. Arbitrary Graphics Objects
  13. Uncategorized For new pages, misplaced pages, etc.

Tree 02:09, 16 Feb 2005 (CST)

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