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== Section Layout ==
*'''See Also: [[OLD_TOPTOC|Old Table of Contents]]'''
Please see [[:Talk:Main Page|Discussion]] for more thoughts on the site organizaiton.
*'''Warning: This page is new and needs more updating.'''
{| style="border: align:center; width:100%; background:#E5DBCF; border: 3px solid #333;"
|-
| 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" | Installation, Configuration & Learning
|-
| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
# '''[[:Category:Installation|Installation]]'''
## [[Linux_Install|Linux]]
## [[MAC_Install|MAC]]
## [[Windows_Install|Windows]]
# '''[[:Category:Stereo 3D Display|Stereo 3D Display]]'''
## [[Linux XFree86 Configuration]]


== PyMolWiki Top-Level Table Of Contents ==
 
# [[:Category:News|News]]
[[Image:0903_1_1.jpg|center|85px]]
# [[:Category:FAQ|Frequently Asked Questions]]
| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
# Brag -- show off your best images or movies.
# '''[[:Category:Using Pymol|Using PyMol]]'''
## News Discussion
## '''[[:Category:Launching|Launching]]'''
## PyMol Beta
### [[Launching PyMOL|Launching PyMOL]]
# [[:Category:Technical Issues|Technical Issues]]
### [[Command_Line_Options|Command Line Options]]
## [[:Category:Installation|Installation]]
### [[Launching_From_a_Script|Launching From a Script]]
### [[Linux_Install|Linux]]
## [[Mouse_Controls|Mouse Controls]]
### [[MAC_Install|MAC]]
## '''[[:Category:Objects and Selections|Objects and Selections]]'''
### [[Windows_Install|Windows]]
### '''[[:Category:Working with Objects|Working with Objects]]'''
# [[Launching PyMOL|Launching PyMOL]]
### '''[[:Category:Working with Selections|Working with Selections]]'''
## Command Line Options
### '''[[:Category:Selector_Quick_Reference|Selector Quick Reference]]'''
## Launching From a Script
# [[:Category:Using Pymol|Using PyMol]]
## Mouse Controls
## [[:Category:Objects and Selections|Objects and Selections]]
### [[:Category:Working with Objects|Working with Objects]]
### [[:Category:Working with Selections|Working with Selections]]
### [[:Category:Selector_Quick_Reference|Selector Quick Reference]]
#### [[Single-word Selectors|Single-word Selectors]]
#### [[Single-word Selectors|Single-word Selectors]]
#### [[Property Selectors|Property Selectors]]
#### [[Property Selectors|Property Selectors]]
#### [[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;"
#### [[Cartoon|Cartoon]]
!style="background:transparent; font-size: 150%; text-decoration:underline; vertical-align:top; text-align:left;"  colspan="2" |  Commands, Representations & Settings
#### [[Surface|Surface]]
|-
#### [[Mesh|Mesh]]
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
#### [[Spheres|Spheres]]
# '''[[:Category:Commands|PyMOL Commands]]'''
#### [[Dots|Dots]]
# '''[[:Category:Settings|Settings (Documented)]]'''
### [[Color|Color]]
## [[Settings|All]]
### [[Displaying Biochemical Properties|Displaying biochemical properties]]
 
## [[:Category:Stereo 3D Display|Stereo 3D Display]] -- wrong place
 
### [[Linux XFree86 Configuration]] -- wrong place
[[Image:050429science.pdf.jpg|85px|center]]
## Scenes
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
## Mouse Settings
# '''[[:Category:Representations|Representations]]'''
## Wizards
## [[Lines|Lines]]
## [[Ray_Tracing|Ray_Tracing]]
## [[Sticks|Sticks]]
## Settings Reference
## [[Ball_and_Stick|Ball and Sticks]]
## Movies and Animations
## [[Cartoon|Cartoon]]
## Structure Alignment
## [[Surface|Surface]]
## Structure Alignment Editor
## [[Mesh|Mesh]]
# [[:Category:Commands|PyMol Commands]]
## [[Spheres|Spheres]]
# [[:Category:Advanced Issues|Advanced Issues]]
## [[Dots|Dots]]
## [[:Category:Modeling and Editing Structures|Modeling and editing structures]]
# '''[[:Category:Coloring|Coloring]]'''
### [[Editing atoms|Editing Atoms]]
## [[Color|Color]]
### [[Molecular Sculpting|Molecular sculpting]]
|}
### [[Homology Modeling|Homology modeling]]
|-
## [[:Category:Image Manipulation|Image Manipulation]]
| align="left" valign="top" |
### labels
{| style="color:#CC9752; padding: 10px; background: transparent;"
### Photoshop/GIMP
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Physico-chemical Modeling
### Stereo Figures
|-
### [[Publication Quality Images|Publication-quality images]]
| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
# [[:Category:Scripting|Scripting]]
# '''[[:Category:Biochemical_Properties|Biochemical Properties]]'''
## [[Displaying Biochemical Properties|Displaying biochemical properties]]
## [[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]]
## [[Example Scripts|Example Scripts]]
## [[Example Scripts|Example Scripts]]
## [[:Category:Script Library|Script Library]]
## '''[[:Category:Script Library|Script Library]]'''
# [[:Category:Plugins|Plugins]]
# '''[[:Category:Plugins|Plugins]]'''
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
## '''[[:Category:Electrostatics|Electrostatics and energy minimization.]]'''
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
### [[APBS|APBS Plugin]]
## rtools
### [[Protein_contact_potential]]
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
## [http://www.rubor.de/bioinf/pymol_extensions.html rtools]
## [[:Category:Plugins Others| Others]]
## [[Plugins_Tutorial|Tutorial on writing plugins]]
|
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
# High-Level Applications
# High-Level Applications
## Crystallography Applications
## Crystallography Applications
Line 72: Line 118:
## NMR Applications
## NMR Applications
### Working with Structure Families
### Working with Structure Families
### Superimposition and RMSD
## '''[[:Category:Structure_Alignment|Superimposition and RMSD]]'''
### NMR Restraints and Analysis
### NMR Restraints and Analysis
# [[:Category:Third Party Software|Third Party Software]]
|}
## [[:Category:PovRay|PovRay]]
| align="left" valign="top" |
## [[:Category:Software Movies|Movies]]
{| style="color:#CC9752; padding: 10px; background: transparent;"
## [[:Category:Software Codecs|Codecs]]
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left; vertical-align:top;" colspan="2"|  Third Party Applications
# [[:Category:Python Integration|Python Integration]]
|-
# [[:Category:PyMol_Integration|PyMol_Integration]] -- adding pymol to other projects (eg OpenGL Object Renderer)
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
# [[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]]
# '''[[: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
## [[:Category:PyMol_Integration Arbitrary_Graphics_Objects|Arbitrary_Graphics_Objects]]
## [[CCTBX|CCTBX]] -- Computational Crystallography Toolbox
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
## [[ProMOL]]
----
## [[S2S]]
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
## '''[[:Category:PyMol_Integration Arbitrary_Graphics_Objects|Arbitrary_Graphics_Objects]]'''
----
|}
|}

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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