TOPTOC: Difference between revisions

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[[OLD_TOPTOC|Old Table of Contents]]
'''See Also: [[OLD_TOPTOC|Old Table of Contents]]'''


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Revision as of 11:15, 15 September 2008

See Also: Old Table of Contents

Installation, Configuration & Learning
  1. Installation
    1. Linux
    2. MAC
    3. Windows
  2. Stereo 3D Display
    1. Linux XFree86 Configuration


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  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


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  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


Ribbon hh1.png
  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


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Extending, Embedding & Scripting
  1. Scripting
    1. Example Scripts
    2. Script Library
  2. Plugins
    1. Electrostatics and energy minimization.
      1. APBS Plugin
      2. Protein_contact_potential
    2. rtools
    3. Tutorial on writing plugins
    4. Others
  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


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  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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