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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 02:46, 20 February 2005

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Section Layout

Please see Discussion for more thoughts on the site organizaiton.