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== Section Layout ==
== Section Layout ==
Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.
Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.
=== Layout Schema ===
# [[:Category:News|News]]
## [[:Category:News Discussion|Discussion]]
## [[:Category:News PyMol Beta|PyMol Beta]]
# [[:Category:Technical Issues|Technical Issues]]
## [[:Category:Technical Issues Installation|Installation]]
### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
# [[:Category:Launching PyMOL|Launching PyMOL]]
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
# [[:Category:Using Pymol|Using PyMol]]
## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
#### [[: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]]
### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
#### [[: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]]
#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
### [[:Category:Using Pymol Objects and Selections Color|Color]]
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
## [[:Category:Using Pymol Display Settings|Display Settings]]
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
### [[Linux XFree86 Configuration]] -- wrong place
## [[:Category:Using Pymol Scenes|Scenes]]
## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
## [[:Category:Using Pymol Wizards|Wizards]]
## [[:Category:Using Pymol Plugins |Plugins]] -- wrong place?
## [[:Category:Using Pymol Ray-tracing|Ray-tracing]]
## [[:Category:Using Pymol Settings Reference|Settings Reference]]
## [[:Category:Using Pymol Movies and Animations|Movies and Animations]]
## [[:Category:Using Pymol Structure Alignment|Structure Alignment]]
## [[:Category:Using Pymol Structure Alignment Editor|Structure Alignment Editor]]
# [[:Category:Commands|Command Language]]
## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
# [[:Category:Advanced Issues|Advanced Issues]]
## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
### [[:Category:Advanced Issues Modeling and Editing Structures Editing atoms|Editing Atoms]]
### [[: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]]
### [[:Category:Advanced Issues Image Manipulation labels|labels]]
### [[:Category:Advanced Issues Image Manipulation Photoshop and GIMP|Photoshop/GIMP]]
### [[:Category:Advanced Issues Image Manipulation Stereo Figures|Stereo Figures]]
### [[:Category:Advanced Issues Image Manipulation Publication Quatlity Images|Publication-quality images]]
# [[:Category:Scripting|Scripting]]
## [[:Category:Scripting Example Scripts|Example Scripts]]
## [[:Category:Scripting Script Library|Script Library]]
# [[:Category:Plugins|Plugins]]
## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
### [[:Category:Plugins Electrostatics and Energy Minimization APBS| APBS Plugin]]
## [[:Category:Plugins rtools | rtools]]
## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
## [[:Category:Plugins Others| Others]]
# [[:Category:High-Level Applications|High-Level Applications]]
## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
### [[:Category:High-Level Applications Symmetry|Symmetry]]
### [[:Category:High-Level Applications Electron Density|Electron Density]]
## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
### [[:Category:High-Level Applications NMR Applications Working with a Family of Structures|Working with Structure Families]]
### [[:Category:High-Level Applications NMR Applications Superimposition and RMSD|Superimposition and RMSD]]
### [[:Category:High-Level Applications NMR Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
# [[:Category:Third Party Software|Third Party Software]]
## [[:Category:Third Party Software Movies|Movies]]
## [[:Category:Third Party Software Codecs|Codecs]]
# [[:Category:Python Integration|Python Integration]]
# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
----
[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
----
=== New! GeShi: Syntax Highlighting for Python & More ===
We now have a syntax highlighter installed.  It now supports something like 28 programming languages!  When you paste your code simply wrap it in
<language_name> ... code here ... </language_name>. 
Here's an example:
<pre>
&lt;python&gt;
  # axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain
# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z
obj = [
  CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
  CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
  CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
  ]
# add labels to axes object (requires pymol version 0.8 or greater, I
# believe
cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
&lt;python&gt;
</pre>
gives us the code
<source lang="python">
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain
# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z
obj = [
  CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
  CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
  CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
  ]
# add labels to axes object (requires pymol version 0.8 or greater, I
# believe
cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
# then we load it into PyMOL
cmd.load_cgo(obj,'axes')
</source>
See [http://qbnz.com/highlighter/index.php The Geshi Home Page]
[[User:Tree|Tree]]

Revision as of 21:46, 19 February 2005

PyMol Wiki Home

You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.


New

Categories/Content

You may now add content to the wiki. This is a semi-structured wiki in that the categories are pseudo-hierarchically linked. If you feel we're missing a category, please find where it would most logically fit, add it to the main page via the Top Level Schema Policy.

Section Layout

Please see Discussion for more thoughts on the site organizaiton.

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