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(Added link to LigAlign.)
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__NOTOC__
 
__NOTOC__
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{| align="center"
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{| align="center" width="90%"
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|+ style="width: 90%; font-size:190%; font-weight: bold; color:#038; text-align:center; padding: 5px; margin-bottom: 15px" | Welcome to the PyMOL Wiki
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|+ style="font-size:190%; font-weight: bold; color:#038; text-align:center; padding: 5px; margin-bottom: 15px" | Welcome to the PyMOL Wiki
 
|- style="text-align:center; font-weight:bold; color: #333; font-size: 120%"
 
|- style="text-align:center; font-weight:bold; color: #333; font-size: 120%"
 
| We are the community-based support site for the popular molecular visualization program, [http://pymol.sf.net PyMOL].
 
| We are the community-based support site for the popular molecular visualization program, [http://pymol.sf.net PyMOL].
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! style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
 
! style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
 
|-
 
|-
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| style="background:#E6EFFF; color:#333; font-size: 110%; padding: 4.5px"| New users are encouraged to [[Special:Userlogin|join]]. Feel free to add any appropriate content; make an account and get started!
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| style="background:#E6EFFF; color:#333; font-size: 110%; padding: 4.5px"| New users are encouraged to [[Special:Userlogin|join]]. Feel free to add any appropriate content; make an account and [[PyMolWiki:Community_Portal|get started]]!
 
|-
 
|-
 
|}
 
|}
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! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
 
! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
 
|-
 
|-
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| [[TOPTOC|'''Table of Contents''']]
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| [[TOPTOC|'''Table of Contents''']] -- ''updated!''
 
|| [[Special:Allpages|Index of all pages]]
 
|| [[Special:Allpages|Index of all pages]]
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|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] [[CheatSheet|Wiki Page]]
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|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] | [[CheatSheet|Wiki Page]]
 
|-
 
|-
 
| [[:Category:Tutorials|Tutorials]]
 
| [[:Category:Tutorials|Tutorials]]
 
|| [[:Category:Commands|Commands]]
 
|| [[:Category:Commands|Commands]]
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|| '''Settings''': [[Settings|All]] [[:Category:Settings|Documented]]
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|| '''Settings''': [[Settings|All]] | [[:Category:Settings|Documented]]
 
|-
 
|-
 
| [[:Category:Script_Library|'''Script Library''']]
 
| [[:Category:Script_Library|'''Script Library''']]
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|-
 
|-
 
| [[:Category:FAQ|Frequently Asked Questions]]
 
| [[:Category:FAQ|Frequently Asked Questions]]
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|| [[PyMolWiki:Community_Portal|'''How to get involved!''']]
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|| [[Gallery|'''Gallery''']] | [[Covers|'''Covers''']]
 
|| [[About| '''About PyMOL''']]
 
|| [[About| '''About PyMOL''']]
 +
|-
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| ''Track:'' [http://sourceforge.net/tracker/?atid=104546&group_id=4546&func=browse Bugs] [http://sourceforge.net/tracker/?group_id=4546&atid=354546 Feature Req] [http://sourceforge.net/tracker/?group_id=4546&atid=204546 Support Req]
 
|-
 
|-
 
|}
 
|}
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
 
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
 
|-
 
|-
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| style="padding: 3px 5px 10px 15px;"| ♦ [http://www.google.com/analytics/ Google Analytics] cookies/tracking added to the wiki.  We're just doing hit counts and watching what people do so we can improve the wiki.
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| style="padding: 3px 5px 10px 15px;"| ♦ New logo for the wiki. It's DNA. You can easily see the major/minor grooves.  If you don't see it, force a reload of the page (CTRL-F5, usually).
 
|-
 
|-
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| style="padding: 3px 5px 10px 15px;"| ♦ [[CheatSheet|PyMOL Cheat Sheet]] (reference card) has been donated.  It's also posted in the table above for quick access.
+
| style="padding: 3px 5px 10px 15px;"| ♦ New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.
 
|-
 
|-
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| style="padding: 3px 5px 10px 15px;"| ♦ '''[[Gsoc2008|Google Summer of Code 2008 for PyMOL]]''' has been created.  '''Update:''' PyMOL wasn't chosen, so this page is now about ideas for improving PyMOL.
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| style="padding: 3px 5px 10px 15px;"| ♦ Information about PyMOL and [[Stereo_3D_Display_Options|Stereo 3D Displays]].
 
|-
 
|-
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| style="padding: 3px 5px 10px 15px;"| ♦ Added a special category/section for active PyMOL [[:Category:Tutorials|Tutorials]].  These are pages not just with information, but easy to understand, step-by-step pages from which to learn.
+
| style="padding: 3px 5px 10px 15px;"| ♦ Massively restructured the [[TOPTOC]] and make the [[OLD_TOPTOC]] for the older version.  Still need to add more content to the [[TOPTOC]].
 +
|-
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| style="padding: 3px 5px 10px 15px;"| ♦ Added a simple script for [[removeAlt|removing specific alternately located atoms]].
 +
|-
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| style="padding: 3px 5px 10px 15px;"| ♦ Added a starter gallery of PyMOL-created Journal [[Covers]].
 +
|-
 +
| style="padding: 3px 5px 10px 15px;"| ♦ Added some information on how PyMOL handles [[Nonstandard_Amino_Acids]].
 +
|-
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| style="padding: 3px 5px 10px 15px;"| &diams; Downtime: The PyMOLWiki underwent some downtime due to FS problems.  There are also upgrades planned for this week, so we may expect a little downtime for that.  We've been <b>very</b> fortunate to have hosting from [http://www.bitgnome.net/ BitGnome.Net]; they've done an incredible job!
 +
|-
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| style="padding: 3px 5px 10px 15px;"| &diams; [[Gallery]] -- Did you make a [[:Image:Ccp4_map.png|cool image]]?  Pop it into the PyMOLWiki Gallery with the PyMOL command you used.  Looking for a particular representation--start here (new!).
 
|}
 
|}
−
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:refcard.png|155px]] Screenshot of the donated [[CheatSheet|PyMOL reference card]].
+
|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:070920nature.pdf.jpg|125px]] Sample Cover from the [[Covers]] gallery.
 
|}
 
|}
 
|-
 
|-
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|-
 
|-
 
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
 
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
 +
|-
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| style="padding: 3px 5px 10px 15px;"| &diams; PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
 
|-
 
|-
 
| style="padding: 3px 5px 10px 15px;"| &diams; [[group]] command has been added.
 
| style="padding: 3px 5px 10px 15px;"| &diams; [[group]] command has been added.
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{|style="background-color: transparent;" width="100%"
 
{|style="background-color: transparent;" width="100%"
 
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts &amp; Plugins
 
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts &amp; Plugins
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|-
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| style="padding: 3px 5px 10px 15px;"| &diams;  [[LigAlign]] -- Ligand-based active site alignment and comparison.
 +
|-
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| style="padding: 3px 5px 10px 15px;"| &diams; Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
 
|-
 
|-
 
| style="padding: 3px 5px 10px 15px;"| &diams; [[ImmersiveViz]] -- Headtracking user interface for PyMOL  (watch the video)!
 
| style="padding: 3px 5px 10px 15px;"| &diams; [[ImmersiveViz]] -- Headtracking user interface for PyMOL  (watch the video)!

Revision as of 22:45, 3 October 2008

Welcome to the PyMOL Wiki
We are the community-based support site for the popular molecular visualization program, PyMOL.


New Users
New users are encouraged to join. Feel free to add any appropriate content; make an account and get started!
Quick Links
Table of Contents -- updated! Index of all pages PyMOL Cheat Sheet: PDF | Wiki Page
Tutorials Commands Settings: All | Documented
Script Library Plugins See All Categories
Frequently Asked Questions Gallery | Covers About PyMOL
Track: Bugs Feature Req Support Req
News and Updates (archive)
Wiki
♦ New logo for the wiki. It's DNA. You can easily see the major/minor grooves. If you don't see it, force a reload of the page (CTRL-F5, usually).
♦ New category about PyMOL performance: making the impossible possible, and the difficult easier/faster.
♦ Information about PyMOL and Stereo 3D Displays.
♦ Massively restructured the TOPTOC and make the OLD_TOPTOC for the older version. Still need to add more content to the TOPTOC.
♦ Added a simple script for removing specific alternately located atoms.
♦ Added a starter gallery of PyMOL-created Journal Covers.
♦ Added some information on how PyMOL handles Nonstandard_Amino_Acids.
♦ Downtime: The PyMOLWiki underwent some downtime due to FS problems. There are also upgrades planned for this week, so we may expect a little downtime for that. We've been very fortunate to have hosting from BitGnome.Net; they've done an incredible job!
♦ Gallery -- Did you make a cool image? Pop it into the PyMOLWiki Gallery with the PyMOL command you used. Looking for a particular representation--start here (new!).
070920nature.pdf.jpg Sample Cover from the Covers gallery.
PyMOL
♦ PyMOL now comes with some builtin examples: look in the examples directory of your source tree.
♦ group command has been added.
♦ The truly awesome grid_mode setting has been added.
♦ Ellipsoids representation added for drawing thermal ellipsoids.
Gm1.png Screenshot of Grid Mode in action.
Scripts & Plugins
♦ LigAlign -- Ligand-based active site alignment and comparison.
♦ Added a simple script for finding the center or mass, or moving a selection to the origin.
♦ ImmersiveViz -- Headtracking user interface for PyMOL (watch the video)!
♦ Colorama --a PyMOL plugin which allows to color objects using adjustable scale bars
♦ ProMOL plugin added. Catalytic site prediction, other tools. Redirects to website.
♦ EMovie plugin added. Easy movies in PyMol using a GUI.
♦ DYNMAP plugin page created. Check it out!
♦ EZ-Viz
COLORAMA-screenshot.jpg Screenshot of Colorama.
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