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[[OLD_TOPTOC|Old Table of Contents]]
*'''See Also: [[OLD_TOPTOC|Old Table of Contents]]'''
 
*'''Warning: This page is new and needs more updating.'''
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# [[:Category:Development|PyMOL Development]]
# [[Scripting|Scripting]]
# [[Scripting|Scripting]]
## [[Example Scripts|Example Scripts]]
## [[Example Scripts|Example Scripts]]
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## [http://www.rubor.de/bioinf/pymol_extensions.html rtools]
## [http://www.rubor.de/bioinf/pymol_extensions.html rtools]
## [[Plugins_Tutorial|Tutorial on writing plugins]]
## [[Plugins_Tutorial|Tutorial on writing plugins]]
## '''[[:Category:Plugins Others| Others]]'''
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Latest revision as of 11:03, 9 September 2010

Installation, Configuration & Learning
  1. Installation
    1. Linux
    2. MAC
    3. Windows
  2. Stereo 3D Display
    1. Linux XFree86 Configuration
  1. Using PyMol
    1. Launching
      1. Launching PyMOL
      2. Command Line Options
      3. Launching From a Script
    2. Mouse Controls
    3. 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
Commands, Representations & Settings
  1. PyMOL Commands
  2. Settings (Documented)
    1. All
  1. Representations
    1. Lines
    2. Sticks
    3. Ball and Sticks
    4. Cartoon
    5. Surface
    6. Mesh
    7. Spheres
    8. Dots
  2. Coloring
    1. Color
Physico-chemical Modeling
  1. Biochemical Properties
    1. Displaying biochemical properties
    2. Surfaces and Voids
  1. Modeling and editing structures
    1. Editing Atoms
    2. Molecular sculpting
    3. Homology modeling
Images & Movies
  1. Image Manipulation
    1. Labels
    2. Photoshop/GIMP
    3. Stereo Figures
    4. Publication-quality images
    5. PovRay
  1. Making Movies
    1. Codecs


Extending, Embedding & Scripting
  1. PyMOL Development
  2. Scripting
    1. Example Scripts
    2. Script Library
  3. Plugins
    1. Electrostatics and energy minimization.
      1. APBS Plugin
      2. Protein_contact_potential
    2. rtools
    3. Tutorial on writing plugins
  1. High-Level Applications
    1. Crystallography Applications
      1. Symmetry|Symmetry
      2. Electron Density
    2. NMR Applications
      1. Working with Structure Families
    3. Superimposition and RMSD
      1. NMR Restraints and Analysis
Third Party Applications
  1. O
  2. SURFNET
  1. Python Integration
  2. PyMol_Integration
    1. Nuccyl -- Nuccyl is a great PyMol extension
    2. CASTp -- Binding and Active site prediction
    3. CCTBX -- Computational Crystallography Toolbox
    4. ProMOL
    5. S2S
    6. Arbitrary_Graphics_Objects
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