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.


Editors, you can upload images for your examples and supporting text!  Check out [[Special:Upload]].
'''Some things to keep in mind''':


=== New! GeShi: Syntax Highlighting for Python & More ===
* You need to [[Special:Userlogin|login]] to edit pages.
'''Update''': I have added the option for numbered syntax highlighting and non-numbered.
* 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.
<pre>
* 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.
<source lang="python">Non line-numbered code here</source>
* Your IP is being tracked.
</pre>
* 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.


<pre>
== Making Edits ==
  <npython>line-numbered code here</npython>
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].
* 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.


Now with line numbers (or not)!
=== Editing ===
* Learn how to insert links.  [[Main_Page|Internal (wiki) links]] and [http://pymol.org/ external links].
** [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]
* Learn how to use sectioning <nowiki>'''==Title=='''</nowiki> is an example.
* Learn how to upload images & insert them into your pages
* Learn how to insert source code:
** Example 1: Python Code
{| 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><source lang="python"></nowiki><br />
<nowiki># your python code goes here</nowiki><br />
<nowiki># for example:</nowiki><br />
<nowiki>for x in cmd.get_names(): print x</nowiki><br />
<nowiki></source></nowiki><br />
| style="padding: 3em;"| <source lang="python">
# your python code goes here
# for example:
for x in cmd.get_names(): print x
</source>
|}
* Example 2: BASH Code with Line Numbers
{| 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><source lang="bash" line="1"></nowiki><br />
<nowiki># your bash code goes here</nowiki><br />
<nowiki># for example:</nowiki><br />
<nowiki>sudo python setup.py install</nowiki><br />
<nowiki>sudo python setup2.py install</nowiki><br />
<nowiki>sudo cp ./pymol /usr/local/bin</nowiki><br />
<nowiki></source></nowiki><br />
| style="padding: 3em;" |<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>
|}
* 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.


<npython>
=== Content ===
# axes.py
* The wiki has lots of technical content.
from pymol.cgo import *
* We need more user-friendly content
from pymol import cmd
** We also need content for non-structural biologists
from pymol.vfont import plain


# create the axes object, draw axes with cylinders coloured red, green,
== What to Do ==
#blue for X, Y and Z
* 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]].
* Each [[:Category:Commands|command]] and [[:Category:Settings|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.


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')
</npython>


== See Also ==
See [http://qbnz.com/highlighter/index.php The Geshi Home Page]


See [http://qbnz.com/highlighter/index.php The Geshi Home Page]
==Paid Documentation?==
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)


[[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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