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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]]


=== Layout Schema ===
 
# [[:Category:News|News]]
[[Image:0903_1_1.jpg|center|85px]]
## [[:Category:News Discussion|Discussion]]
| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
## [[:Category:News PyMol Beta|PyMol Beta]]
# '''[[:Category:Using Pymol|Using PyMol]]'''
# [[:Category:Technical Issues|Technical Issues]]
## '''[[:Category:Launching|Launching]]'''
## [[:Category:Technical Issues Installation|Installation]]
### [[Launching PyMOL|Launching PyMOL]]
### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
### [[Command_Line_Options|Command Line Options]]
#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
### [[Launching_From_a_Script|Launching From a Script]]
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
## [[Mouse_Controls|Mouse Controls]]
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
## '''[[:Category:Objects and Selections|Objects and Selections]]'''
# [[:Category:Launching PyMOL|Launching PyMOL]]
### '''[[:Category:Working with Objects|Working with Objects]]'''
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
### '''[[:Category:Working with Selections|Working with Selections]]'''
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
### '''[[:Category:Selector_Quick_Reference|Selector Quick Reference]]'''
# [[:Category:Using Pymol|Using PyMol]]
#### [[Single-word Selectors|Single-word Selectors]]
## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
#### [[Property Selectors|Property Selectors]]
## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
#### [[Selection Algebra|Selection Algebra]]
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
#### [[Selection Macros|Selection Macros]]
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
|}
### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
| align="left" valign="top" |
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
{| style="color:#CC9752; padding: 10px; background: transparent;"
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
!style="background:transparent; font-size: 150%; text-decoration:underline; vertical-align:top; text-align:left;"  colspan="2" |  Commands, Representations & Settings
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]
|-
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
# '''[[:Category:Commands|PyMOL Commands]]'''
#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
# '''[[:Category:Settings|Settings (Documented)]]'''
#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
## [[Settings|All]]
#### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]
 
#### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]
 
#### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]
[[Image:050429science.pdf.jpg|85px|center]]
#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
# '''[[:Category:Representations|Representations]]'''
### [[:Category:Using Pymol Objects and Selections Color|Color]]
## [[Lines|Lines]]
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
## [[Sticks|Sticks]]
## [[:Category:Using Pymol Display Settings|Display Settings]]
## [[Ball_and_Stick|Ball and Sticks]]
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
## [[Cartoon|Cartoon]]
### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
## [[Surface|Surface]]
### [[Linux XFree86 Configuration]] -- wrong place
## [[Mesh|Mesh]]
## [[:Category:Using Pymol Scenes|Scenes]]
## [[Spheres|Spheres]]
## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
## [[Dots|Dots]]
## [[:Category:Using Pymol Wizards|Wizards]]
# '''[[:Category:Coloring|Coloring]]'''
## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]
## [[Color|Color]]
## [[:Category:Using Pymol Settings Reference|Settings Reference]]
|}
## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]
|-
## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]
| align="left" valign="top" |
## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]
{| style="color:#CC9752; padding: 10px; background: transparent;"
# [[:Category:Commands|Command Language]]
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Physico-chemical Modeling
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
|-
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
# [[:Category:Advanced Issues|Advanced Issues]]
# '''[[:Category:Biochemical_Properties|Biochemical Properties]]'''
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
## [[Displaying Biochemical Properties|Displaying biochemical properties]]
### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]
## [[Surfaces_and_Voids|Surfaces and Voids]]
### [[:Category:Advanced Issues Modeling and Editing Structures Molecular Sculpting|Molecular sculpting]]
 
### [[:Category:Advanced Issues Modeling and Editing Structures Homology Modeling|Homology modeling]]
 
## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
[[Image:Ribbon_hh1.png|center|85px]]
### [[:Category:Advanced Issues Image Manipulation labels|labels]]
| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]
# [[Modeling_and_Editing_Structures|Modeling and editing structures]]
### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]
## [[Editing atoms|Editing Atoms]]
### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]
## [[Molecular Sculpting|Molecular sculpting]]
# [[:Category:Scripting|Scripting]]
## [[Homology Modeling|Homology modeling]]
## [[:Category:Scripting Example Scripts|Example Scripts]]
|}
## [[:Category:Scripting Script Library|Script Library]]
| align="left" valign="top" |
# [[:Category:Plugins|Plugins]]
{| style="color:#CC9752; padding: 10px; background: transparent;"
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left; vertical-align:top;" colspan="2" | Images & Movies
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
|-
## [[:Category:Plugins rtools | rtools]]
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
# '''[[:Category:Image Manipulation|Image Manipulation]]'''
## [[:Category:Plugins Others| Others]]
## [[Label|Labels]]
# [[:Category:High-Level Applications|High-Level Applications]]
## Photoshop/GIMP
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
## [[Stereo_Ray|Stereo Figures]]
### [[:Category:High-Level Applications Symmetry|Symmetry]]
## [[Publication Quality Images|Publication-quality images]]
### [[:Category:High-Level Applications Electron Density|Electron Density]]
## [[PovRay|PovRay]]
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
|
### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]
# [[Making_Movies|Making Movies]]
### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
## [[Software_Codecs|Codecs]]
# [[:Category:Third Party Software|Third Party Software]]
 
## [[:Category:Third Party Software PovRay|PovRay]]
 
## [[:Category:Third Party Software Movies|Movies]]
[[Image:070816nature.pdf.jpg|center|85px]]
## [[:Category:Third Party Software Codecs|Codecs]]
|}
# [[:Category:Python Integration|Python Integration]]
|-
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
| align="left" valign="top" |
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
{| style="color:#CC9752; padding: 10px; background: transparent;"
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Extending, Embedding & Scripting
----
|-
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
----
# [[:Category:Development|PyMOL Development]]
# [[Scripting|Scripting]]
## [[Example Scripts|Example Scripts]]
## '''[[:Category:Script Library|Script Library]]'''
# '''[[:Category:Plugins|Plugins]]'''
## '''[[:Category:Electrostatics|Electrostatics and energy minimization.]]'''
### [[APBS|APBS Plugin]]
### [[Protein_contact_potential]]
## [http://www.rubor.de/bioinf/pymol_extensions.html rtools]
## [[Plugins_Tutorial|Tutorial on writing plugins]]
|
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
# High-Level Applications
## Crystallography Applications
### Symmetry|Symmetry
### Electron Density
## NMR Applications
### Working with Structure Families
## '''[[:Category:Structure_Alignment|Superimposition and RMSD]]'''
### NMR Restraints and Analysis
|}
| 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"|  Third Party Applications
|-
| 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
## [[CASTp|CASTp]] -- Binding and Active site prediction
## [[CCTBX|CCTBX]] -- Computational Crystallography Toolbox
## [[ProMOL]]
## [[S2S]]
## '''[[: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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