Difference between revisions of "Main Page"

Latest revision as of 03:21, 22 June 2021

hosted by

Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org

Quick Links
Tutorials	Table of Contents	Commands
Script Library	Plugins	FAQ
Gallery \| Covers	PyMOL Cheat Sheet (PDF)	Getting Help

News & Updates
Official Release	PyMOL v2.5 has been released on May 10, 2021.
Python 3	New Python 3 compatibility guide for scripts and plugins
POSF	New PyMOL fellows announced for 2018-2019
Tutorial	Plugins Tutorial updated for PyQt5
New Plugin	PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
Selection keywords	New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update	MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script	dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
Older News	See Older News.

Did you know...
Xpyder xPyder is a PyMOL plugin for analyzing coupled residued and their networks in proteins. You can download it here.

A Random PyMOL-generated Cover. See Covers.

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 __NOTOC__
-{| align="center" width="90%"
+{| align="center" width="100%" style="background: #B22222; margin-bottom: 4em; border-bottom: 1px solid #B22222; border-left: 1px solid #B22222; border-right: 1px solid #B22222;"
-|+ style="font-size:190%; font-weight: bold; color:#038; text-align:center; padding: 5px; margin-bottom: 15px" | Welcome to the PyMOL Wiki
+|+ style="font-size: 1.0em; font-weight: normal; color: #FFFFFF; text-align:right; background: #B22222; padding-top:0.5em; padding-bottom: 0.25em; padding-right: 0.60em; border-top: 2px solid #B22222; border-bottom: 1px solid #fff;" |hosted by [[File:SBGridlogo2.jpg|140 px|link=https://sbgrid.org/]]
-|- 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].
-|-
 |}
-{| align="center" style="width:90%; margin-bottom: 20px"
+{| align="center" style="padding-bottom: 3em;"
-|
+|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
-{| align="left" width="20%" style="border: 1px solid #333; text-align:center; height=100%;"
+|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
-! style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
+| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
-|-
+|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
-| 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]]!
+| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
-|-
+|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
 |}
-{| align="right" width="75%" style="border: 1px solid #333; text-align:left;"
-! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
+{| align="center" width="45%" style="background: #FFFFFF; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
-|-
+|+ style="font-size: 1.4em; font-weight: bold; color: #FFFFFF; text-align:center; background: #000000; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #000000; border-bottom: 1px solid #fff;" |Quick Links
-| [[TOPTOC|'''Table of Contents''']]
+|-
-|| [[Special:Allpages|Index of all pages]]
+| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
-|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] | [[CheatSheet|Wiki Page]]
-|-
-| [[:Category:Tutorials|Tutorials]] <font color='red'><b>!</b></font>
-|| [[:Category:Commands|Commands]]
-|| '''Settings''': [[Settings|All]]  | [[:Category:Settings|Documented]]
-|-
-| [[:Category:Script_Library|'''Script Library''']] <font color='red'><b>!</b></font>
-|| [[:Category:Plugins|'''Plugins''']]
-|| [[:Special:Categories| See All Categories]]
-|-
-| [[:Category:FAQ|Frequently Asked Questions]]
-|| [[Gallery|'''Gallery''']] | [[Covers|'''Covers''']]
-|| [[About| '''About PyMOL''']]
-|-
-| ''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]
-|-
-|}
-|- style="color: #333; font-weight:bold; font-size: 20px; text-align:center; padding: 10em;"
-|
-<!--
-[http://www.pymol.org/ PyMOL 1.2] has been released! -->
-|
-|}
-{| 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="background-color: transparent;" width="100%"
-|-
-|valign="top"|
-{|style="background-color: transparent;" width="100%"
-|-
-! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
-|-
-| style="padding: 2px 5px 0px 15px;"| &diams; '''[http://www.pymol.org/ PyMOL] 1.2 is out!
-|-
-| style="padding: 2px 5px 0px 15px;"| &diams; Check out the artist who integrates PyMOL into [http://winkleman.com/artist/seriesview/1406/376 his work].
 |-
-| 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]].
+| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
 |-
-| style="padding: 2px 5px 0px 15px;"| &diams; '''PyMOL now integrates seamlessly with MS Powerpoint.  See [[Axpymol]].'''
+| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
-|}
+||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
-|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Image_large.png|125px]] Another cover made with PyMOL.'''Movie made with Pymol of MD simulation of protein-prtein interaction'''is avialble inside pdf [[http://www.pymolwiki.org/index.php/File:SH3.pdf]] or High quality AVI [http://gepard.bioinformatik.uni-saarland.de/old_html/material/dl/SH3_large.avi] .
+||'''[[PyMOL_mailing_list|Getting Help]]'''
 |}
+{| width="100%"
+| style="vertical-align: top; width: 40%" |
+{| class="jtable" style="float: left; width: 90%;"
+|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
 |-
-|
+! Official Release
-{|style="background-color: transparent;" width="100%"
+| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
-|-
-|valign="top"|
-{|style="background-color: transparent;" width="100%"
-! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts, Plugins &amp; Tutorials
 |-
-| style="padding: 2px 5px 0px 15px;"| &diams; [[MovieSchool]] &mdash; PyMOL Wiki's Movie School.  Learn how to make movies in PyMOL!
+! Python 3
+| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 |-
-| style="padding: 2px 5px 0px 15px;"| &diams; [[alphaToAll]] &mdash; Expands your desired alpha-carbon property down to all atoms in the residue.
+! POSF
+| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 |-
-| style="padding: 2px 5px 0px 15px;"| &diams; [[interfaceResidues]] &mdash; Finds interface residues in a complex.
+! Tutorial
+| [[Plugins Tutorial]] updated for PyQt5
 |-
-| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSurfaceResidues]] &mdash; Find and show (if you want) surface exposed resiues in PyMOL.
+! New Plugin
+| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
 |-
-| style="padding: 2px 5px 0px 15px;"| &diams; [[ToGroup]] &mdash; Converts a multistate object into a group of single state objects.
+! Selection keywords
+| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
 |-
-| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSeq]] &mdash; Find sequence or regular expression of amino acids in a protein.
+! Plugin Update
+| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 |-
-| 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.
+! New Script
+| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
 |-
-| style="padding: 2px 5px 0px 15px;"| &diams; [[Pucker]] &mdash; finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
+! Older News
-|}
+| See [[Older_News|Older News]].
-|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:DrawMinBB.png|165px]] Screenshot of [[DrawBoundingBox]] in action.
 |}
-{|style="background-color: transparent;" width="100%"
+|style="vertical-align: top; width: 40%"|
+{| class="jtable" style="float: right; width: 90%"
+|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
 |-
-|valign="top"|
+|<div class="didyouknow" >
-{|style="background-color: transparent;" width="100%"
+<DynamicPageList>
-|-
+randomcount=1
-! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
+category=Commands|Plugins|Script_Library|Settings
-|-
+includepage=*
-| style="padding: 2px 5px 0px 15px;"| &diams; [[Label]]s page was thoroughly refurbished.
+includemaxlength=1050
-|-
+escapelinks=false
-| style="padding: 2px 5px 0px 15px;"| &diams; The Wiki experienced a few moments of downtime due to system maintenance.  The downtime was <10 minutes.
+allowcachedresults=false
-|-
+resultsheader=__NOTOC__ __NOEDITSECTION__
-| 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.
+listseparators=,<h3>[[%PAGE%]]</h3>,,\n
-|-
+</DynamicPageList>
-| 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.
+</div>
-|-
+<div style="clear: both;"></div>
-| style="padding: 2px 5px 0px 15px;"| &diams; We got our '''2,000,000th''' page view!
-|}
-|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:Science090410.jpg|125px]] Sample Cover from the [[Covers]] gallery.
 |}
+|
+|style="vertical-align: top; width: 18%"|
+<DynamicPageList>
+imagecontainer=Covers
+randomcount=1
+escapelinks=false
+openreferences=true
+listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
+ordermethod=none
+allowcachedresults=false
+</DynamicPageList>
 |}

Difference between revisions of "Main Page"

Latest revision as of 03:21, 22 June 2021

Xpyder

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