|
|
| Line 10: |
Line 10: |
| == 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>
| |
| <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')
| |
|
| |
| <python>
| |
| </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]]
| |