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== Notes ==
 +
Each major link should link to a category page.  Then, each category page should have a short intro and the auto-generated out-going links to each of its pages.  This way, we get coverage with minimal effort.
  
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== New Table ==
 +
Here's the code for a new table for this page.  This page is quite popular and needs to be cleaned up...alot.  Feel free to make changes to the main TOPTOC as needed.
 +
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{| style="border: align:center; width:100%; background:#E5DBCF; border: 3px solid #333;"
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|-
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| align="left" valign="top" |
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{| style="color:#CC9752; padding: 10px; background: transparent;"
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!  style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Installation, Configuration & Learning
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|-
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| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
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# '''[[:Category:Installation|Installation]]'''
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## [[Linux_Install|Linux]]
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## [[MAC_Install|MAC]]
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## [[Windows_Install|Windows]]
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# '''[[:Category:Stereo 3D Display|Stereo 3D Display]]'''
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## [[Linux XFree86 Configuration]]
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 +
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[[Image:0903_1_1.jpg|center|85px]]
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| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
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# '''[[:Category:Using Pymol|Using PyMol]]'''
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## '''[[:Category:Launching|Launching]]'''
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### [[Launching PyMOL|Launching PyMOL]]
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### [[Command_Line_Options|Command Line Options]]
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### [[Launching_From_a_Script|Launching From a Script]]
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## [[Mouse_Controls|Mouse Controls]]
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## '''[[:Category:Objects and Selections|Objects and Selections]]'''
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### '''[[:Category:Working with Objects|Working with Objects]]'''
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### '''[[:Category:Working with Selections|Working with Selections]]'''
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### '''[[:Category:Selector_Quick_Reference|Selector Quick Reference]]'''
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#### [[Single-word Selectors|Single-word Selectors]]
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#### [[Property Selectors|Property Selectors]]
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#### [[Selection Algebra|Selection Algebra]]
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#### [[Selection Macros|Selection Macros]]
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|}
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| align="left" valign="top" |
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{| style="color:#CC9752; padding: 10px; background: transparent;"
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!style="background:transparent; font-size: 150%; text-decoration:underline; vertical-align:top; text-align:left;"  colspan="2" |  Commands, Representations & Settings
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|-
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| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
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# '''[[:Category:Commands|PyMOL Commands]]'''
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# '''[[:Category:Settings|Settings (Documented)]]'''
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## [[Settings|All]]
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 +
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[[Image:050429science.pdf.jpg|85px|center]]
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| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
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# '''[[:Category:Representations|Representations]]'''
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## [[Lines|Lines]]
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## [[Sticks|Sticks]]
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## [[Ball_and_Stick|Ball and Sticks]]
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## [[Cartoon|Cartoon]]
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## [[Surface|Surface]]
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## [[Mesh|Mesh]]
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## [[Spheres|Spheres]]
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## [[Dots|Dots]]
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# '''[[:Category:Coloring|Coloring]]'''
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## [[Color|Color]]
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|}
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|-
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| align="left" valign="top" |
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{| style="color:#CC9752; padding: 10px; background: transparent;"
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! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left;" colspan="2" | Physico-chemical Modeling
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|-
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| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
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# '''[[:Category:Biochemical_Properties|Biochemical Properties]]'''
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## [[Displaying Biochemical Properties|Displaying biochemical properties]]
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## [[Surfaces_and_Voids|Surfaces and Voids]]
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 +
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[[Image:Ribbon_hh1.png|center|85px]]
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| style="background:transparent; color: #333; width:50%; font-weight: normal; font-size:100%; text-align:left; vertical-align:top;"|
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# [[Modeling_and_Editing_Structures|Modeling and editing structures]]
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## [[Editing atoms|Editing Atoms]]
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## [[Molecular Sculpting|Molecular sculpting]]
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## [[Homology Modeling|Homology modeling]]
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|}
 +
| 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
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|-
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| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
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# '''[[:Category:Image Manipulation|Image Manipulation]]'''
 +
## [[Label|Labels]]
 +
## Photoshop/GIMP
 +
## [[Stereo_Ray|Stereo Figures]]
 +
## [[Publication Quality Images|Publication-quality images]]
 +
## [[PovRay|PovRay]]
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|
 +
| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
 +
# [[Making_Movies|Making Movies]]
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## [[Software_Codecs|Codecs]]
 +
 +
 +
[[Image:070816nature.pdf.jpg|center|85px]]
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|}
 +
|-
 +
| 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;"|
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# [[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]
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## [[Plugins_Tutorial|Tutorial on writing plugins]]
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## '''[[:Category:Plugins Others| Others]]'''
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|
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| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
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# 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;"
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! style="background:transparent; font-size: 150%; text-decoration:underline; text-align:left; vertical-align:top;" colspan="2"|  Third Party Applications
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|-
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| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
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# [[O]]
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# [[SURFNET]]
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 +
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[[Image:080602cnen.pdf.jpg|center|85px]]
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|
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| style="background:transparent; color: #333; width:50%; text-align:left; vertical-align:top;"|
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# [[Python_Integration|Python Integration]]
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# '''[[: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
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## [[ProMOL]]
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## [[S2S]]
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## '''[[:Category:PyMol_Integration Arbitrary_Graphics_Objects|Arbitrary_Graphics_Objects]]'''
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|}
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|}

Latest revision as of 00:44, 28 March 2014

Notes

Each major link should link to a category page. Then, each category page should have a short intro and the auto-generated out-going links to each of its pages. This way, we get coverage with minimal effort.

New Table

Here's the code for a new table for this page. This page is quite popular and needs to be cleaned up...alot. Feel free to make changes to the main TOPTOC as needed.

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. 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


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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