PyMOLWiki:Community Portal - Revision history

Pyadmin: 33 revisions

2014-03-28T00:49:19Z

33 revisions

New page

= Get Involved =
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.

'''Some things to keep in mind''':

* You need to [[Special:Userlogin|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 [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.

=== 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> 
<nowiki># your python code goes here</nowiki> 
<nowiki># for example:</nowiki> 
<nowiki>for x in cmd.get_names(): print x</nowiki> 
<nowiki></source></nowiki> 
| 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> 
<nowiki># your bash code goes here</nowiki> 
<nowiki># for example:</nowiki> 
<nowiki>sudo python setup.py install</nowiki> 
<nowiki>sudo python setup2.py install</nowiki> 
<nowiki>sudo cp ./pymol /usr/local/bin</nowiki> 
<nowiki></source></nowiki> 
| 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> 
| 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.

=== 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 [[: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.

== See Also ==
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)

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)

Warren: /* Paid documentation? */

2007-11-13T02:51:13Z

Paid documentation?

Guaka at 12:28, 5 September 2007

2007-09-05T12:28:10Z

New page

= How to Get Involved =
* First, go sign up, if you don't already have an account. New accounts can be created from any page; see the upper right hand side of any given page.

== What to Do ==
* If you have a powerful little script you wrote and enjoy using, upload it and let the world know about it.
* Each of the commands, needs many many nice examples of 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.

== Features ==
=== New! GeShi: Syntax Highlighting for Python & More ===
Use Geshi for syntax highlighting your Python code! '''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>

Now with line numbers (or not)!

<npython>
# 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')
</npython>

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)

Wgscott: /* How to Get Involved */

2006-02-15T20:02:58Z

How to Get Involved

New page

= How to Get Involved =
* First, go request and account (see [[Main_Page]]).

== What to Do ==
* Next, we need folks to clean up the commands.
* If you have a nifty script, feel free to upload it and add an index to your entry on the main page.
* We need examples included with the commands.

== Features ==
=== New! GeShi: Syntax Highlighting for Python & More ===
Use Geshi for syntax highlighting your Python code! '''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>

Now with line numbers (or not)!

<npython>
# 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')
</npython>

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

2chemp at 21:18, 14 November 2005

2005-11-14T21:18:11Z

Show changes

Krother at 14:05, 23 March 2005

2005-03-23T14:05:56Z

Tree at 07:19, 2 March 2005

2005-03-02T07:19:35Z

Tree: /* New! GeShi: Syntax Highlighting for Python & More */

2005-03-02T07:17:50Z

New! GeShi: Syntax Highlighting for Python & More

Tree: /* Helping */

2005-03-02T07:17:31Z

Helping

Tree: /* Section Layout */

2005-03-02T06:26:42Z

Section Layout

← Older revision		Revision as of 02:51, 13 November 2007
Line 52:		Line 52:


−	==Paid ~~documentation~~?==	+	==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)		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)
		+
		+	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)

← Older revision		Revision as of 14:05, 23 March 2005
Line 4:		Line 4:
	Editors, you can upload images for your examples and supporting text! Check out [[Special:Upload]].		Editors, you can upload images for your examples and supporting text! Check out [[Special:Upload]].

		+	== Working with Categories ==
		+	To assign pages to categories, use tags at the end of your page containing the category, sub-category and the page name.
		+
		+	Example: There is a page 'Publication Quality Images' in the category 'Advanced Issues' and the sub-category 'Image Manipulation'. It has the tag:
		+	<pre>
		+	[[Category:Advanced_Issues_Image_Manipulation\|Publication Quality Images]]
		+	</pre>

	== Helping ==		== Helping ==

@@ Line 1: / Line 1: @@
 == CP ==
 Look here for ways to get involved in the PyMolWiki!
 == Helping ==

@@ Line 3: / Line 3: @@
 == Helping ==
 * 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]].
 === New! GeShi: Syntax Highlighting for Python & More ===
@@ Line 21: / Line 15: @@
   <npython>line-numbered code here</npython>
 </pre>
 Now with line numbers!

@@ Line 11: / Line 11: @@
 You may now add content to the wiki.  This is a semi-structured wiki in that the categories are pseudo-hierarchically linked.
 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]].
 === New! GeShi: Syntax Highlighting for Python & More ===