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__NOTOC__
__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;"
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|+ 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]]!
| If you want to contribute new content to this wiki, request an account by emailing  accounts (@) sbgrid dot org from your '''institutional''' email address.
|-
|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
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{| 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]]
| 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]]'''
|| [[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="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]]'')
||'''[[PyMOL_mailing_list|Getting Help]]'''
|}
|}
|- style="color: #333; font-weight:bold; font-size: 20px; text-align:center; padding: 10em;"
 
|  
{| width="100%"
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[http://www.pymol.org/ PyMOL 1.2] has been released! -->
{| 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 &amp; Updates
|}
{| 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"|
! New Setup
{|style="background-color: transparent;" width="100%"
| [https://github.com/kullik01/pymol-open-source-windows-setup/releases/tag/v3.1.0 PyMOL-open-source-windows-setup v3.1] has been released on January 20, 2025. More information under [[Windows Install]].
|-
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
! New Plugin
| [[PySSA]] aims to combine PyMOL and [https://github.com/sokrypton/ColabFold ColabFold] to enable the prediction and analysis of 3D protein structures for the scientific end-user. [https://github.com/urban233/PySSA/releases/tag/v1.0.1 v1.0 has been released] on July 10, 2024.
|-
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[Space]]&mdash; new command to control PyMOL's usage of color spaces.
! Official Release
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[CGOCylinder]]&mdash; information on CGO cylinders and circles in PyMOL.
! New Plugin
| [[CavitOmiX|CavitOmiX]] calculate [https://innophore.com Catalophore™ cavities], predict protein structures with [https://www.nvidia.com/en-us/gpu-cloud/bionemo OpenFold by NVIDIA-BioNeMo], [https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/ ESMFold] and retrieve [https://www.deepmind.com/research/highlighted-research/alphafold Alphafold] models
|-
|-
| style="padding: 2px 5px 0px 15px;"| &diams; '''[http://www.pymol.org/ PyMOL] 1.2 is out!
! Official Release
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
|-
| style="padding: 2px 5px 0px 15px;"| &diams; Check out the artist who integrates PyMOL into [http://winkleman.com/artist/seriesview/1406/376 his work].
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
| 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]].
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
| style="padding: 2px 5px 0px 15px;"| &diams; '''PyMOL now integrates seamlessly with MS Powerpoint.  See [[Axpymol]].'''
! Tutorial
|}
| [[Plugins Tutorial]] updated for PyQt5
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Image_large.png|125px]] Another cover made with PyMOL.  See [[User:Mazen|image details]].
|}
|-
|-
|
! New Plugin
{|style="background-color: transparent;" width="100%"
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
|-
|valign="top"|
! Selection keywords
{|style="background-color: transparent;" width="100%"
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
! 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; [[CgoCircle]]&mdash; draw CGO circles in PyMOL; surround objects or selections with circles.
! 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 0px 15px;"| &diams; [[MovieSchool]] &mdash; PyMOL Wiki's Movie School.  Learn how to make movies in PyMOL!
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[alphaToAll]] &mdash; Expands your desired alpha-carbon property down to all atoms in the residue.
! Older News
|-
| See [[Older_News|Older News]].
| style="padding: 2px 5px 0px 15px;"| &diams; [[interfaceResidues]] &mdash; Finds interface residues in a complex.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSurfaceResidues]] &mdash; Find and show (if you want) surface exposed resiues in PyMOL.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[ToGroup]] &mdash; Converts a multistate object into a group of single state objects.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSeq]] &mdash; Find sequence or regular expression of amino acids in a protein.
|-
| 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.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[Pucker]] &mdash; finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
|}
|}
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:DrawMinBB.png|165px]] Screenshot of [[DrawBoundingBox]] in action.
|style="vertical-align: top; width: 40%"|
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{| class="jtable" style="float: right; width: 90%"
{|style="background-color: transparent;" width="100%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[Label]]s page was thoroughly refurbished.
|-
| 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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| 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.
|<div class="didyouknow" >
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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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Latest revision as of 15:10, 27 April 2026

hosted by
Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
If you want to contribute new content to this wiki, request an account by emailing accounts (@) sbgrid dot org from your institutional email address.
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
New Setup PyMOL-open-source-windows-setup v3.1 has been released on January 20, 2025. More information under Windows Install.
New Plugin PySSA aims to combine PyMOL and ColabFold to enable the prediction and analysis of 3D protein structures for the scientific end-user. v1.0 has been released on July 10, 2024.
Official Release PyMOL v3.0 has been released on March 12, 2024.
New Plugin CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models
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 fellowship announced for 2022-2023
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...

Commands

Commands are functions in pymol that are used for viewing, manipulating, and storing molecules.

You can get a list of some common commands by typing "help commands" into the pymol command line. Typing this in to version 1.1r1 returns the following: 

   INPUT/OUTPUT  load      save      delete    quit
   VIEW          turn      move      clip      rock
                 show      hide      enable    disable
                 reset     refresh   rebuild   
                 zoom      origin    orient   
                 view      get_view  set_view
   MOVIES        mplay     mstop     mset      mdo
                 mpng      mmatrix   frame
                 rewind    middle    ending
                 forward   backward
   IMAGING       png       mpng
   RAY TRACING   ray       
   MAPS          isomesh   isodot
   DISPLAY       cls       viewport  splash    
   SELECTIONS    select    mask   
   SETTINGS      set       button
   ATOMS         alter     alter_state 
   EDITING       create    ..→
A Random PyMOL-generated Cover. See Covers.


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