PyMOLWiki:Community Portal: Difference between revisions

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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.


=== New! GeShi: Syntax Highlighting for Python & More ===
== Making Edits ==
'''Update''': I have added the option for numbered syntax highlighting and non-numbered.
Please feel free to upload ideas, suggestions, scripts, images, examples, hints, tips -- you name it.  If it's PyMOL-related, we'll take it!
<pre>
* Learn how to use MediaWiki.  See [http://meta.wikimedia.org/wiki/Help:Editing MediaWiki's Editing Page].
  <source lang="python">Non line-numbered code here</source>
* Feel free to upload images (even big ones).
</pre>
** 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.


<pre>
=== Editing ===
  <npython>line-numbered code here</npython>
* Learn how to insert links. [[Main_Page|Internal (wiki) links]] and [http://pymol.org/ external links].
</pre>
** [http://meta.wikimedia.org/wiki/Help:Link Link Documentation]
 
* Learn how to link to a category and also how to make a page a part of a category.
 
** [http://meta.wikimedia.org/wiki/Help:Category Category Documentation]
We now have a syntax highlighter installed. It now supports something like 28 programming languages!  When you paste your code simply wrap it in
* Learn how to use sectioning <nowiki>'''==Title=='''</nowiki> is an example.
&lt;language_name&gt; ... code here ... &lt;/language_name&gt;. 
* Learn how to upload images & insert them into your pages
 
* Learn how to insert source code:
Here's an example:
** Example 1: Python Code
<pre>
{| align="center"
&lt;python&gt;
! style="font-size:150%; text-decoration:underline; text-align: center;" | You Type || style="font-size:150%; text-decoration:underline; text-align:center"| We See
  # axes.py
|-
from pymol.cgo import *
| style="padding: 3em;" |<nowiki><source lang="python"></nowiki><br />
from pymol import cmd
<nowiki># your python code goes here</nowiki><br />
from pymol.vfont import plain
<nowiki># for example:</nowiki><br />
 
<nowiki>for x in cmd.get_names(): print x</nowiki><br />
# create the axes object, draw axes with cylinders coloured red, green,
<nowiki></source></nowiki><br />
#blue for X, Y and Z
| style="padding: 3em;"| <source lang="python">
 
# your python code goes here
obj = [
# for example:
  CYLINDER, 0., 0., 0., 50., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
for x in cmd.get_names(): print x
  CYLINDER, 0., 0., 0., 0., 50., 0., 0.2, 1.0, 1.0, 1.0, 0., 1.0, 0.,
</source>
  CYLINDER, 0., 0., 0., 0., 0., 50., 0.2, 1.0, 1.0, 1.0, 0., 0.0, 1.0,
|}
  ]
* Example 2: BASH Code with Line Numbers
 
{| align="center"
# add labels to axes object (requires pymol version 0.8 or greater, I
! style="font-size:150%; text-decoration:underline; text-align: center;" | You Type || style="font-size:150%; text-decoration:underline; text-align:center"| We See
# believe
|-
 
|style="padding: 3em;" | <nowiki><source lang="bash" line="1"></nowiki><br />
cyl_text(obj,plain,[-5.,-5.,-1],'Origin',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
<nowiki># your bash code goes here</nowiki><br />
cyl_text(obj,plain,[50.,0.,0.],'X',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
<nowiki># for example:</nowiki><br />
cyl_text(obj,plain,[0.,50.,0.],'Y',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
<nowiki>sudo python setup.py install</nowiki><br />
cyl_text(obj,plain,[0.,0.,50.],'Z',0.20,axes=[[3,0,0],[0,3,0],[0,0,3]])
<nowiki>sudo python setup2.py install</nowiki><br />
 
<nowiki>sudo cp ./pymol /usr/local/bin</nowiki><br />
# then we load it into PyMOL
<nowiki></source></nowiki><br />
cmd.load_cgo(obj,'axes')
| style="padding: 3em;" |<source lang="bash" line="1">
 
# your bash code goes here
&lt;python&gt;
# for example:
</pre>
sudo python setup.py install
 
sudo python setup2.py install
gives us the code
sudo cp ./pymol /usr/local/bin
<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 22:59, 3 October 2008

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>

 
# your bash code goes here
# for example:
sudo python setup.py install
sudo python setup2.py install
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>
  • 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)

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