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(Added link to LigAlign.)
 
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{| align="center" width="90%" style="background: #fafafa; border-right: 1px solid #333; border-left: 1px solid #333; border-bottom: 1px solid #333"
 
{| align="center" width="90%" style="background: #fafafa; border-right: 1px solid #333; border-left: 1px solid #333; border-bottom: 1px solid #333"
 
|+ style="text-align: left; font-weight:bold; font-size:150%; color:#333; background: #EFE6FF; padding:10px; border: 1px solid #333" | News and Updates ([[Older_News|archive]])
 
|+ style="text-align: left; font-weight:bold; font-size:150%; color:#333; background: #EFE6FF; padding:10px; border: 1px solid #333" | News and Updates ([[Older_News|archive]])
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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;"| ♦ 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;"| ♦ Documented a few more settings.  Also, check out the cool, [[Huge_surfaces]] page for handling very large objects and representing them as surfaces, in PyMOL.
 
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| 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;"| ♦ We got our '''2,000,000th''' page view!
 
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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 links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests.
 
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| 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;"| ♦ 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;"| ♦ Added a simple script for [[removeAlt|removing specific alternately located atoms]].
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| 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;"| ♦ Added a starter gallery of PyMOL-created Journal [[Covers]].
 
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| 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!).
 
 
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|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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|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:080701_h.a.steinberg_biochemie.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 integrates seamlessly with MS Powerpoint.  See [[Axpymol]].'''
 
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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; PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
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| style="padding: 3px 5px 10px 15px;"| &diams; [[Ellipsoids]] representation added for drawing thermal ellipsoids.
 
| style="padding: 3px 5px 10px 15px;"| &diams; [[Ellipsoids]] representation added for drawing thermal ellipsoids.
 
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|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Gm1.png|125px]] Screenshot of [[grid_mode|Grid Mode]] in action.
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|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Caver.png|125px]] Screenshot of [[Caver]] showing cavities.
 
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! 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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| 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; [[GetNamesInSel]] &#8212; find the names of all objects in a selection.
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| style="padding: 3px 5px 10px 15px;"| &diams; [[CalcArea]] &#8212; find the area of any given object/selection;
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| style="padding: 3px 5px 10px 15px;"| &diams; [[ConnectedCloud]] &#8212; find connected clouds of objects in PyMOL.
 
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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.
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| style="padding: 3px 5px 10px 15px;"| &diams; [[MakeVinaCommand]] &#8212; Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.
 
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| style="padding: 3px 5px 10px 15px;"| &diams; [[ImmersiveViz]] -- Headtracking user interface for PyMOL  (watch the video)!
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| style="padding: 3px 5px 10px 15px;"| &diams; [[DrawBoundingBox]] &#8212; Draw a bounding box around your selection.
 
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| style="padding: 3px 5px 10px 15px;"| &diams; [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars
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| style="padding: 3px 5px 10px 15px;"| &diams; Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
 
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| style="padding: 3px 5px 10px 15px;"| &diams; [http://ase-web.rit.edu/~ez-viz/ProMOL_dl.html ProMOL] plugin added.  Catalytic site prediction, other tools.  Redirects to website.
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| style="padding: 3px 5px 10px 15px;"| &diams; Ever wanted to load all the PDBs in a directory within PyMOL?  Now you can load all files in a dir with [[LoadDir]].
 
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| style="padding: 3px 5px 10px 15px;"| &diams; [[EMovie]] plugin added.  Easy movies in PyMol using a GUI.
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| style="padding: 3px 5px 10px 15px;"| &diams; [[PDB Web Services Script]] &#8212; Example using PyMOL and the PDB Web Services.
 
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| style="padding: 3px 5px 10px 15px;"| &diams; [[DYNMAP]] plugin page created. Check it out!
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| style="padding: 3px 5px 10px 15px;"| &diams; [[LigAlign]] &#8212; Ligand-based active site alignment and comparison.
 
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| style="padding: 3px 5px 10px 15px;"| &diams; [[EZ-Viz]]
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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.
 
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|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:COLORAMA-screenshot.jpg|125px]] Screenshot of [[Colorama]].
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|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:DrawMinBB.png|165px]] Screenshot of [[DrawBoundingBox]] in action.
 
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Revision as of 19:11, 30 March 2009

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
♦ Documented a few more settings. Also, check out the cool, Huge_surfaces page for handling very large objects and representing them as surfaces, in PyMOL.
♦ We got our 2,000,000th page view!
♦ Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests.
♦ 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.
080701 h.a.steinberg biochemie.jpg Sample Cover from the Covers gallery.
PyMOL
♦ PyMOL now integrates seamlessly with MS Powerpoint. See Axpymol.
♦ 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.
Caver.png Screenshot of Caver showing cavities.
Scripts & Plugins
♦ GetNamesInSel — find the names of all objects in a selection.
♦ CalcArea — find the area of any given object/selection;
♦ ConnectedCloud — find connected clouds of objects in PyMOL.
♦ MakeVinaCommand — Use PyMOL to create a valid command line for the new Vina docking software.
♦ DrawBoundingBox — Draw a bounding box around your selection.
♦ Locate loaded PyMOL objects that are nearby some other object with FindObjectsNearby.
♦ Ever wanted to load all the PDBs in a directory within PyMOL? Now you can load all files in a dir with LoadDir.
♦ PDB Web Services Script — Example using PyMOL and the PDB Web Services.
♦ 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.
DrawMinBB.png Screenshot of DrawBoundingBox in action.
Retrieved from "http://wiki.pymol.org/index.php?title=Main_Page&oldid=4688"