TOPTOC: Difference between revisions

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# '''[[:Category:News|News]]'''
*'''See Also: [[OLD_TOPTOC|Old Table of Contents]]'''
# '''[[:Category:FAQ|Frequently Asked Questions]]'''
*'''Warning: This page is new and needs more updating.'''
# [[Gallery]] -- PyMOL Gallery and HOWTO
{| style="border: align:center; width:100%; background:#E5DBCF; border: 3px solid #333;"
# '''[[:Category:Technical Issues|Technical Issues]]'''
|-
## '''[[:Category:Installation|Installation]]'''
| align="left" valign="top" |
### [[Linux_Install|Linux]]
{| style="color:#CC9752; padding: 10px; background: transparent;"
### [[MAC_Install|MAC]]
!  style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Installation, Configuration & Learning
### [[Windows_Install|Windows]]
|-
# '''[[:Category:Launching|Launching]]'''
| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
## [[Launching PyMOL|Launching PyMOL]]
# '''[[:Category:Installation|Installation]]'''
## [[Command_Line_Options|Command Line Options]]
## [[Linux_Install|Linux]]
## [[Launching_From_a_Script|Launching From a Script]]
## [[MAC_Install|MAC]]
## [[Windows_Install|Windows]]
# '''[[:Category:Stereo 3D Display|Stereo 3D Display]]'''
## [[Linux XFree86 Configuration]]
 
 
[[Image:0903_1_1.jpg|center|85px]]
| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
# '''[[:Category:Using Pymol|Using PyMol]]'''
# '''[[:Category:Using Pymol|Using PyMol]]'''
## '''[[:Category:Launching|Launching]]'''
### [[Launching PyMOL|Launching PyMOL]]
### [[Command_Line_Options|Command Line Options]]
### [[Launching_From_a_Script|Launching From a Script]]
## [[Mouse_Controls|Mouse Controls]]
## [[Mouse_Controls|Mouse Controls]]
## '''[[:Category:Objects and Selections|Objects and Selections]]'''
## '''[[:Category:Objects and Selections|Objects and Selections]]'''
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#### [[Selection Algebra|Selection Algebra]]
#### [[Selection Algebra|Selection Algebra]]
#### [[Selection Macros|Selection Macros]]
#### [[Selection Macros|Selection Macros]]
### '''[[:Category:Representations|Representations]]'''
|}
#### [[Lines|Lines]]
| align="left" valign="top" |
#### [[Sticks|Sticks]]
{| style="color:#CC9752; padding: 10px; background: transparent;"
#### [[Ball_and_Stick|Ball and Sticks]]
!style="background:transparent; font-size: 150%; text-decoration:underline; vertical-align:top; text-align:left;"  colspan="2" |  Commands, Representations & Settings
#### [[Cartoon|Cartoon]]
|-
#### [[Surface|Surface]]
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
#### [[Mesh|Mesh]]
# '''[[:Category:Commands|PyMOL Commands]]'''
#### [[Spheres|Spheres]]
# '''[[:Category:Settings|Settings (Documented)]]'''
#### [[Dots|Dots]]
## [[Settings|All]]
## '''[[:Category:Coloring|Coloring]]'''
 
### [[Color|Color]]
 
## '''[[:Category:Biochemical_Properties|Biochemical Properties]]'''
[[Image:050429science.pdf.jpg|85px|center]]
### [[Displaying Biochemical Properties|Displaying biochemical properties]]
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
## '''[[:Category:Stereo 3D Display|Stereo 3D Display]]''' -- wrong place
# '''[[:Category:Representations|Representations]]'''
### [[Linux XFree86 Configuration]] -- wrong place
## [[Lines|Lines]]
## Scenes
## [[Sticks|Sticks]]
## Mouse Settings
## [[Ball_and_Stick|Ball and Sticks]]
## Wizards
## [[Cartoon|Cartoon]]
## [[Ray_Tracing|Ray_Tracing]]
## [[Surface|Surface]]
## [[Settings]] Reference
## [[Mesh|Mesh]]
## [http://www.pymolwiki.org/index.php/Special:Search?search=movie&go=Go Movies and Animations Topics]
## [[Spheres|Spheres]]
## ''[[:Category:Structure_Alignment|Structure Alignment]]'''
## [[Dots|Dots]]
## Structure Alignment Editor
# '''[[:Category:Coloring|Coloring]]'''
# '''[[:Category:Commands|PyMol Commands]]'''
## [[Color|Color]]
# '''[[:Category:Advanced Issues|Advanced Issues]]'''
|}
## [[Modeling_and_Editing_Structures|Modeling and editing structures]]
|-
### [[Editing atoms|Editing Atoms]]
| align="left" valign="top" |
### [[Molecular Sculpting|Molecular sculpting]]
{| style="color:#CC9752; padding: 10px; background: transparent;"
### [[Homology Modeling|Homology modeling]]
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Physico-chemical Modeling
## '''[[:Category:Image Manipulation|Image Manipulation]]'''
|-
### [[Label|Labels]]
| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
### Photoshop/GIMP
# '''[[:Category:Biochemical_Properties|Biochemical Properties]]'''
### [[Stereo_Ray|Stereo Figures]]
## [[Displaying Biochemical Properties|Displaying biochemical properties]]
### [[Publication Quality Images|Publication-quality images]]
## [[Surfaces_and_Voids|Surfaces and Voids]]
 
 
[[Image:Ribbon_hh1.png|center|85px]]
| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
# [[Modeling_and_Editing_Structures|Modeling and editing structures]]
## [[Editing atoms|Editing Atoms]]
## [[Molecular Sculpting|Molecular sculpting]]
## [[Homology Modeling|Homology modeling]]
|}
| align="left" valign="top" |
{| style="color:#CC9752; padding: 10px; background: transparent;"
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left; vertical-align:top;" colspan="2" | Images & Movies
|-
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
# '''[[:Category:Image Manipulation|Image Manipulation]]'''
## [[Label|Labels]]
## Photoshop/GIMP
## [[Stereo_Ray|Stereo Figures]]
## [[Publication Quality Images|Publication-quality images]]
## [[PovRay|PovRay]]
|
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
# [[Making_Movies|Making Movies]]
## [[Software_Codecs|Codecs]]
 
 
[[Image:070816nature.pdf.jpg|center|85px]]
|}
|-
| align="left" valign="top" |
{| style="color:#CC9752; padding: 10px; background: transparent;"
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Extending, Embedding & Scripting
|-
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
# [[: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]]'''
|
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
# High-Level Applications
# High-Level Applications
## Crystallography Applications
## Crystallography Applications
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## '''[[:Category:Structure_Alignment|Superimposition and RMSD]]'''
## '''[[:Category:Structure_Alignment|Superimposition and RMSD]]'''
### NMR Restraints and Analysis
### NMR Restraints and Analysis
# '''[[:Category:Third Party Software|Third Party Software]]'''
|}
## [[PovRay|PovRay]]
| align="left" valign="top" |
## [[Making_Movies|Making Movies]]
{| style="color:#CC9752; padding: 10px; background: transparent;"
## [[Software_Codecs|Codecs]]
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left; vertical-align:top;" colspan="2"|  Third Party Applications
## [[Surfaces_and_Voids|Surfaces and Voids]]
|-
## [[O]]
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
## [[SURFNET]]
# [[O]]
# [[SURFNET]]
 
 
[[Image:080602cnen.pdf.jpg|center|85px]]
|
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
# [[Python_Integration|Python Integration]]
# [[Python_Integration|Python Integration]]
# '''[[:Category:PyMol_Integration|PyMol_Integration]]''' -- adding pymol to other projects (eg OpenGL Object Renderer)
# '''[[:Category:PyMol_Integration|PyMol_Integration]]'''
## [[Nuccyl|Nuccyl]] -- Nuccyl is a great PyMol extension
## [[Nuccyl|Nuccyl]] -- Nuccyl is a great PyMol extension
## [[CASTp|CASTp]] -- Binding and Active site prediction
## [[CASTp|CASTp]] -- Binding and Active site prediction
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## [[S2S]]
## [[S2S]]
## '''[[:Category:PyMol_Integration Arbitrary_Graphics_Objects|Arbitrary_Graphics_Objects]]'''
## '''[[:Category:PyMol_Integration Arbitrary_Graphics_Objects|Arbitrary_Graphics_Objects]]'''
# '''[[:Category:Uncategorized|Uncategorized]]''' For new pages, misplaced pages, etc.
|}
|}

Latest revision as of 06:03, 9 September 2010

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


0903 1 1.jpg
  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


050429science.pdf.jpg
  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


070816nature.pdf.jpg
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


080602cnen.pdf.jpg
  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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