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== CP ==
+
= Get Involved =
Look here for ways to get involved in the PyMolWiki!
+
First, [[Special:Userlogin|Create a New Account or Login]].  We have to block anonymous users from editing pages because too many spammers were abusing the system.  Signing up is easy, fast & free.
  
== Helping ==
+
'''Some things to keep in mind''':
* A wiki edit/user policy is needed.
 
* Graphic design and CSS layout: We need logos, BG images and CSS layout
 
* Importing the email list content:  We have (lots) of email to sift through, extract data from and import into the Wiki
 
* If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].
 
  
=== Categories/Content ===
+
* You need to [[Special:Userlogin|login]] to edit pages.
You may now add content to the wiki.  This is a semi-structured wiki in that the categories are pseudo-hierarchically linked.   
+
* Each page on the wiki has a Discussion page (even this page)You access it by clicking on the "Discussion" tab at the top of the page.  Discussion pages are where we discuss changes to any particular page.  If you'd like to make a change, but don't want to ruin a page, make comments about your updates in its discussion page.
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]].
+
* Each user has his or her own home page.  Once you've logged in, just click on your name in the upper right hand corner.  People can leave you messages by posting that message on your Discussion page.
 +
* Your IP is being tracked.
 +
* Your changes are being tracked.  You can easily see everyone's changes, and undo them if they're inappropriate.  This helps us reduce spam.
 +
* We want you to help make edits and keep the content relevant & fresh!
 +
* Don't worry about making errors in your edits.
 +
** You can preview your edits to make sure they're correct before submitting;
 +
** We typically watch the content and clean up after folks if we need to.
  
== Section Layout ==
+
== Making Edits ==
Please see [[:Talk:Main Page|Discussion]] for more thoughts on the site organizaiton.
+
Please feel free to upload ideas, suggestions, scripts, images, examples, hints, tips -- you name it.  If it's PyMOL-related, we'll take it!
 +
* Learn how to use MediaWiki.  See [http://meta.wikimedia.org/wiki/Help:Editing MediaWiki's Editing Page].
 +
* Feel free to upload images (even big ones).
 +
** Be warned, you have to agree that you own the image and are releasing it under a certain open license.  You must agree to this before uploading the images.
 +
** If you do not own the image or have permission to post it, please don't.
  
=== Layout Schema ===
+
=== Editing ===
# [[:Category:News|News]]
+
* Learn how to insert links.  [[Main_Page|Internal (wiki) links]] and [http://pymol.org/ external links].
## [[:Category:News Discussion|Discussion]]
+
** [http://meta.wikimedia.org/wiki/Help:Link Link Documentation]
## [[:Category:News PyMol Beta|PyMol Beta]]
+
* Learn how to link to a category and also how to make a page a part of a category.
# [[:Category:Technical Issues|Technical Issues]]
+
** [http://meta.wikimedia.org/wiki/Help:Category Category Documentation]
## [[:Category:Technical Issues Installation|Installation]]
+
* Learn how to use sectioning <nowiki>'''==Title=='''</nowiki> is an example.
### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
+
* Learn how to upload images & insert them into your pages
#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
+
* Learn how to insert source code:
#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
+
** Example 1: Python Code
#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
+
{| align="center"
# [[:Category:Launching PyMOL|Launching PyMOL]]
+
! style="font-size:150%; text-decoration:underline; text-align: center;" | You Type || style="font-size:150%; text-decoration:underline; text-align:center"| We See
## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
+
|-  
## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
+
| style="padding: 3em;" |<nowiki><source lang="python"></nowiki><br />
# [[:Category:Using Pymol|Using PyMol]]
+
<nowiki># your python code goes here</nowiki><br />
## [[:Category:Using Pymol Mouse Controls|Mouse Controls]]
+
<nowiki># for example:</nowiki><br />
## [[:Category:Using Pymol Objects and Selections|Objects and Selections]]
+
<nowiki>for x in cmd.get_names(): print x</nowiki><br />
### [[:Category:Using Pymol Objects and Selections Working with Objects|Working with Objects]]
+
<nowiki></source></nowiki><br />
### [[:Category:Using Pymol Objects and Selections Working with Selections|Working with Selections]]
+
| style="padding: 3em;"| <source lang="python">
### [[:Category:Using Pymol Objects and Selections Selector Quick Reference|Selector Quick Reference]]
+
# your python code goes here
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Single-word Selectors|Single-word Selectors]]
+
# for example:
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Property Selectors|Property Selectors]]
+
for x in cmd.get_names(): print x
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Algebra|Selection Algebra]]
+
</source>
#### [[:Category:Using Pymol Objects and Selections Selector Quick Reference Selection Macros|Selection Macros]]
+
|}
### [[:Category:Using Pymol Objects and Selections Representations|Representations]]
+
* Example 2: BASH Code with Line Numbers
#### [[:Category:Using Pymol Objects and Selections Representations Lines|Lines]]
+
{| align="center"
#### [[:Category:Using Pymol Objects and Selections Representations Sticks|Sticks]]
+
! style="font-size:150%; text-decoration:underline; text-align: center;" | You Type || style="font-size:150%; text-decoration:underline; text-align:center"| We See
#### [[:Category:Using Pymol Objects and Selections Representations Cartoon|Cartoon]]
+
|-
#### [[:Category:Using Pymol Objects and Selections Representations Surface|Surface]]
+
|style="padding: 3em;" | <nowiki><source lang="bash" line="1"></nowiki><br />
#### [[:Category:Using Pymol Objects and Selections Representations Mesh|Mesh]]
+
<nowiki># your bash code goes here</nowiki><br />
#### [[:Category:Using Pymol Objects and Selections Representations Spheres|Spheres]]
+
<nowiki># for example:</nowiki><br />
#### [[:Category:Using Pymol Objects and Selections Representations Dots|Dots]]
+
<nowiki>sudo python setup.py install</nowiki><br />
### [[:Category:Using Pymol Objects and Selections Color|Color]]
+
<nowiki>sudo python setup2.py install</nowiki><br />
### [[:Category:Using Pymol Objects and Selections Displaying Biochemical Properties|Displaying biochemical properties]]
+
<nowiki>sudo cp ./pymol /usr/local/bin</nowiki><br />
## [[:Category:Using Pymol Display Settings|Display Settings]]
+
<nowiki></source></nowiki><br />
## [[:Category:Using Pymol Stereo 3D Display|Stereo 3D Display]] -- wrong place
+
| style="padding: 3em;" |<source lang="bash" line="1">
### [[:Category:Using Pymol Hardware Options|Hardware Options]] -- wrong place?
+
# your bash code goes here
### [[Linux XFree86 Configuration]] -- wrong place
+
# for example:
## [[:Category:Using Pymol Scenes|Scenes]]
+
sudo python setup.py install
## [[:Category:Using Pymol Mouse Settings|Mouse Settings]]
+
sudo python setup2.py install
## [[:Category:Using Pymol Wizards|Wizards]]
+
sudo cp ./pymol /usr/local/bin
## [[: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 PovRay|PovRay]]
 
## [[: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 ===
 
'''Update''': I have added the option for numbered syntax highlighting and non-numbered.
 
<pre>
 
<source lang="python">Non line-numbered code here</source>
 
</pre>
 
 
 
<pre>
 
<npython>line-numbered code here</npython>
 
</pre>
 
 
 
 
 
We now have a syntax highlighter installed.  It now supports something like 28 programming languages!  When you paste your code simply wrap it in
 
&lt;language_name&gt; ... code here ... &lt;/language_name&gt;. 
 
 
 
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>
 
</source>
 +
|}
 +
* Learn how to insert math.  It's formatted in [http://meta.wikimedia.org/wiki/Help:Formula LaTeX]:
 +
{| align="center"
 +
! style="font-size:150%; text-decoration:underline; text-align: center;" | You Type || style="font-size:150%; text-decoration:underline; text-align:center"| We See
 +
|-
 +
| style="padding: 3em;" |<nowiki><math>dist(A,B) = \sqrt { \sum_i { \left( A_i - B_i \right)^2 } }</math></nowiki><br />
 +
| style="padding: 3em;" |<math>dist(i,j) = \sqrt{ \sum_i { \left( A_i - B_i \right)^2 } }</math>
 +
|}
 +
* Learn how to write tables.  This is more advanced & takes a bit to time to learn & a lifetime to master.
  
Now with line numbers!
+
=== Content ===
 +
* The wiki has lots of technical content.
 +
* We need more user-friendly content
 +
** We also need content for non-structural biologists
  
<npython>
+
== What to Do ==
  # axes.py
+
* If you have a powerful little script you wrote and enjoy using, upload it and let the world know about it.  Go to the [[:Category:Script_Library|Script Library]].
from pymol.cgo import *
+
* Each [[:Category:Commands|command]] and [[:Category:Settings|setting]] needs nice example usage. Feel free to expound (and comment on) the commands.
from pymol import cmd
+
* More internal linking (from page to page) is needed.
from pymol.vfont import plain
+
* We also need a way to make things easier to find on the wiki.
 +
* More categories and organization within categories would be nice.
  
# 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
+
== See Also ==
# believe
+
See [http://qbnz.com/highlighter/index.php The Geshi Home Page]
  
cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
+
==Paid Documentation?==
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
+
I might be interested in using PyMOL, but I don't like the fact that I have to pay for documentation. I don't even know what I'm missing out on, and I don't know if it's worth trying out PyMOL, or becoming actively involved in its development (or simply the creation of content on this wiki). [[User:Guaka|Guaka]] 07:28, 5 September 2007 (CDT)
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')
 
</npython>
 
 
 
 
 
See [http://qbnz.com/highlighter/index.php The Geshi Home Page]
 
  
[[User:Tree|Tree]]
+
Huh?  You don't have to pay for documentation. PyMOLWiki is freely accessible, and it contains far more useful content than the "official" docs.  You can also easily try out PyMOL without compiling the current open-source code by downloading older [http://delsci.com/rel/099 free builds] or the current [http://delsci.com/eval evaluation build].  Nobody ''has'' to pay for PyMOL -- it's open source!  [[User:Warren|Warren]] 20:51, 12 November 2007 (CST)

Latest revision as of 00:49, 28 March 2014

Get Involved

First, Create a New Account or Login. We have to block anonymous users from editing pages because too many spammers were abusing the system. Signing up is easy, fast & free.

Some things to keep in mind:

  • You need to login to edit pages.
  • Each page on the wiki has a Discussion page (even this page). You access it by clicking on the "Discussion" tab at the top of the page. Discussion pages are where we discuss changes to any particular page. If you'd like to make a change, but don't want to ruin a page, make comments about your updates in its discussion page.
  • Each user has his or her own home page. Once you've logged in, just click on your name in the upper right hand corner. People can leave you messages by posting that message on your Discussion page.
  • Your IP is being tracked.
  • Your changes are being tracked. You can easily see everyone's changes, and undo them if they're inappropriate. This helps us reduce spam.
  • We want you to help make edits and keep the content relevant & fresh!
  • Don't worry about making errors in your edits.
    • You can preview your edits to make sure they're correct before submitting;
    • We typically watch the content and clean up after folks if we need to.

Making Edits

Please feel free to upload ideas, suggestions, scripts, images, examples, hints, tips -- you name it. If it's PyMOL-related, we'll take it!

  • Learn how to use MediaWiki. See MediaWiki's Editing Page.
  • Feel free to upload images (even big ones).
    • Be warned, you have to agree that you own the image and are releasing it under a certain open license. You must agree to this before uploading the images.
    • If you do not own the image or have permission to post it, please don't.

Editing

You Type We See
<source lang="python">

# your python code goes here
# for example:
for x in cmd.get_names(): print x
</source>

# your python code goes here
# for example:
for x in cmd.get_names(): print x
  • Example 2: BASH Code with Line Numbers
You Type We See
<source lang="bash" line="1">

# your bash code goes here
# for example:
sudo python setup.py install
sudo python setup2.py install
sudo cp ./pymol /usr/local/bin
</source>

1 # your bash code goes here
2 # for example:
3 sudo python setup.py install
4 sudo python setup2.py install
5 sudo cp ./pymol /usr/local/bin
  • Learn how to insert math. It's formatted in LaTeX:
You Type We See
<math>dist(A,B) = \sqrt { \sum_i { \left( A_i - B_i \right)^2 } }</math>
<math>dist(i,j) = \sqrt{ \sum_i { \left( A_i - B_i \right)^2 } }</math>
  • Learn how to write tables. This is more advanced & takes a bit to time to learn & a lifetime to master.

Content

  • The wiki has lots of technical content.
  • We need more user-friendly content
    • We also need content for non-structural biologists

What to Do

  • If you have a powerful little script you wrote and enjoy using, upload it and let the world know about it. Go to the Script Library.
  • Each command and setting needs nice example usage. Feel free to expound (and comment on) the commands.
  • More internal linking (from page to page) is needed.
  • We also need a way to make things easier to find on the wiki.
  • More categories and organization within categories would be nice.


See Also

See The Geshi Home Page

I might be interested in using PyMOL, but I don't like the fact that I have to pay for documentation. I don't even know what I'm missing out on, and I don't know if it's worth trying out PyMOL, or becoming actively involved in its development (or simply the creation of content on this wiki). Guaka 07:28, 5 September 2007 (CDT)

Huh? You don't have to pay for documentation. PyMOLWiki is freely accessible, and it contains far more useful content than the "official" docs. You can also easily try out PyMOL without compiling the current open-source code by downloading older free builds or the current evaluation build. Nobody has to pay for PyMOL -- it's open source! Warren 20:51, 12 November 2007 (CST)