Difference between revisions of "Main Page"

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{| align="center" width="90%"
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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!
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{| align="center" style="padding-bottom: 4em;"
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|- style="text-align:center; font-weight:bold; color: #333; font-size: 120%"
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|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 7px" | Welcome to the PyMOL Wiki!
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| ''The community-run support site for the [http://pymol.org PyMOL] molecular viewer.''
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|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
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|-
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| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
 
|}
 
|}
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{| align="center" style="width:90%; margin-bottom: 20px"
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{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
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{| align="left" width="20%" style="border: 1px solid #333; text-align:center; height=100%;"
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|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links
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! style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
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|-
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| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
 
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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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| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
 
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| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
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||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
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||'''[[GoogleSearch]]'''
 
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{| align="right" width="75%" style="border: 1px solid #333; text-align:left;"
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! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
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{| class="jtable" style="float: left; width: 90%;"
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
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|-
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| [[TOPTOC|'''Table of Contents''']]
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! Warren
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|| [[Special:Allpages|Index of all pages]]
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| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
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|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] | [[CheatSheet|Wiki Page]]
 
 
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| [[:Category:Tutorials|Tutorials]] <font color='red'><b>!</b></font>
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! PyMOLWiki
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|| [[:Category:Commands|Commands]]
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| Reformatted Main Page.
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|| '''Settings''': [[Settings|All]]  | [[:Category:Settings|Documented]]
 
 
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|-
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| [[:Category:Script_Library|'''Script Library''']] <font color='red'><b>!</b></font>
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! PyMOLWiki
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|| [[:Category:Plugins|'''Plugins''']]
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| New &mdash; Search the PyMOLWiki via [[GoogleSearch]]
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|| [[:Special:Categories| See All Categories]]
 
 
|-
 
|-
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| [[:Category:FAQ|Frequently Asked Questions]]
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! PyMOL
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|| [[Gallery|'''Gallery''']] | [[Covers|'''Covers''']]
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| PyMOL is known to work under Mac OS X 10+ (Snow Leopard) using the new Fink and incentive builds.  See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].
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|| [[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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! PyMOL
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|| '''[[GoogleSearch]]''' <font color='red'><b>!</b></font>
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| PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
 
|-
 
|-
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! PyMOL
 +
| [[Space]]&mdash; new command to control PyMOL's usage of color spaces.
 
|}
 
|}
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|- style="color: #333; font-weight:bold; font-size: 20px; text-align:center; padding: 10em;"
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|style="vertical-align: top; width: 40%"|
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|
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{| class="jtable" style="float: right; width: 90%"
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News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]]. <br />
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Do you know this PyMOL command...
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|
 
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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"
 
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|+ 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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|valign="top"|
 
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{|style="background-color: transparent;" width="100%"
 
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|-
 
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | New &mdash; Search the PyMOLWiki via [[GoogleSearch]]
 
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|-
 
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; PyMOL is known to work under Mac OS X 10+ (Snow Leopard) using the new Fink and incentive builds.  See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[Space]]&mdash; new command to control PyMOL's usage of color spaces.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[CGOCylinder]]&mdash; information on CGO cylinders and circles in PyMOL.
 
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| style="padding: 2px 5px 0px 15px;"| &diams; '''[http://www.pymol.org/ PyMOL] 1.2 is out!
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; Check out the artist who integrates PyMOL into [http://winkleman.com/artist/seriesview/1406/376 his work].
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; If you use the sequence viewer alot, or have lots of openGL text on the screen, try boosting your performance with [[Texture_fonts]].
 
 
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|-
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| style="padding: 2px 5px 0px 15px;"| &diams; '''PyMOL now integrates seamlessly with MS Powerpoint.  See [[Axpymol]].'''
+
|<div class="didyouknow" >
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<dpl>
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namespace=
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category=Commands
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includepage=*
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includemaxlength=300
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escapelinks=false
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resultsheader=__NOTOC__ __NOEDITSECTION__
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randomcount=1
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mode=userformat
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addpagecounter=true
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listseparators=,<h3>[[%PAGE%]]</h3>,,\n
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</dpl>
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</div>
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<div style="clear: both;"></div>
 
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|valign="middle" width="150px" style="padding: 0 20px 20px 0" |[[Image:SuperSymExample2.png|135px]] Example image from [[SuperSym]], showing cell, symmetry mates and symmetry axes.
 
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{|style="background-color: transparent;" width="100%"
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|style="vertical-align: top; width: 18%"|
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<dpl>
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|valign="top"|
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imagecontainer=Covers
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{|style="background-color: transparent;" width="100%"
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randomcount=1
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts, Plugins &amp; Tutorials
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escapelinks=false
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|-
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openreferences=true
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| style="padding: 2px 5px 0px 15px;"| &diams; [[Save2traj]] &mdash; plugin for saving objects to a dcd trajectory file!
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listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n
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|-
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</dpl>
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| style="padding: 2px 5px 0px 15px;"| &diams; [[SuperSym]] &mdash; plugin for visualizing lots and lots of space groups!
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[Autodock_Plugin]] &mdash; New PyMOL plugin for interacting with AutoDock (including AutoDock Vina) and visualizing results.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[Spectrumbar]] &mdash; powerful new script for making custom spectrum bars in PyMOL.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[CollapseSel]] &mdash; simple script to compress selection lists: eg. instead of i. 1+2+3+4+5 you get 1-5.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[CgoCircle]] &mdash; draw CGO circles in PyMOL; surround objects or selections with circles.
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[MovieSchool]] &mdash; PyMOL Wiki's Movie School.  Learn how to make movies in PyMOL!
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[alphaToAll]] &mdash; Expands your desired alpha-carbon property down to all atoms in the residue.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[interfaceResidues]] &mdash; Finds interface residues in a complex.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSurfaceResidues]] &mdash; Find and show (if you want) surface exposed resiues in PyMOL.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[ToGroup]] &mdash; Converts a multistate object into a group of single state objects.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSeq]] &mdash; Find sequence or regular expression of amino acids in a protein.
 
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|-
 
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| style="padding: 2px 5px 10px 15px;"| &diams; [[Modevectors]] &mdash; creates arrow plots for normal mode analysis (NMA), NMR ensembles and other cases where you want to point out differences between similar objects.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[Pucker]] &mdash; finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
 
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|}
 
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|valign="middle" width="150px" style="padding: 0 20px 20px 0" |[[Image:Sb_default.png|165px]] Example image from the new script, [[Spectrumbar]].
 
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{|style="background-color: transparent;" width="100%"
 
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|valign="top"|
 
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{|style="background-color: transparent;" width="100%"
 
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; Added the new [[GoogleSearch]] widget for better searching on the wiki.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; [[Label]]s page was thoroughly refurbished.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; The Wiki experienced a few moments of downtime due to system maintenance.  The downtime was <10 minutes.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; '''Please note the "Go" and "Search" buttons in the search bar.  They're not the same, and entering text and hitting ENTER is the same as using the "Go" button.'''  Please try using the "Search" button; we're using a new search engine and it has cool new features.
 
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|-
 
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| style="padding: 2px 5px 0px 15px;"| &diams; 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: 2px 5px 0px 15px;"| &diams; We got our '''2,000,000th''' page view!
 
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|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:Science090410.jpg|125px]] Sample Cover from the [[Covers]] gallery.
 
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Revision as of 13:03, 17 November 2009


Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) GoogleSearch


News & Updates
Warren News about Warren DeLano's passing may be read on Warren's memorial page.
PyMOLWiki Reformatted Main Page.
PyMOLWiki New — Search the PyMOLWiki via GoogleSearch
PyMOL PyMOL is known to work under Mac OS X 10+ (Snow Leopard) using the new Fink and incentive builds. See Installing PyMOL under Fink.
PyMOL PyMOL now has a Set command for basic settings, and a Set_bond command for bond-only settings.
PyMOL Space— new command to control PyMOL's usage of color spaces.
Do you know this PyMOL command...

The DPL extension (version 2.3.0) produced a SQL statement which lead to a Database error.
The reason may be an internal error of DPL or an error which you made,
especially when using DPL options like titleregexp.
Query text is:
SELECT DISTINCT `pmw_page`.page_namespace AS page_namespace,`pmw_page`.page_title AS page_title,`pmw_page`.page_id AS page_id, `pmw_page`.page_title AS sortkey, `pmw_page`.page_counter AS page_counter FROM `pmw_page` INNER JOIN `pmw_categorylinks` AS cl0 ON `pmw_page`.page_id=cl0.cl_from AND (cl0.cl_to='Commands') WHERE 1=1 AND `pmw_page`.page_namespace IN (0) AND `pmw_page`.page_is_redirect=0 ORDER BY page_title ASC LIMIT 500 OFFSET 0

Error message is:
Unknown column 'pmw_page.page_counter' in 'field list' (localhost)


The DPL extension (version 2.3.0) produced a SQL statement which lead to a Database error.
The reason may be an internal error of DPL or an error which you made,
especially when using DPL options like titleregexp.
Query text is:
SELECT DISTINCT ic.il_to, ic.il_to AS sortkey FROM `pmw_imagelinks` AS ic WHERE 1=1 AND (ic.il_from=2199) ORDER BY pl_title ASC LIMIT 500 OFFSET 0

Error message is:
Unknown column 'pl_title' in 'order clause' (localhost)


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=7423"