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__NOTOC__
__NOTOC__
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{| 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]]!
| To request a new account, email SBGrid at: accounts (@) sbgrid dot org
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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;"
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|+ 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]]
|| [[:Category:Commands|Commands]]
|| '''Settings''': [[Settings|All]] | [[:Category:Settings|Documented]]
|-
| [[:Category:Script_Library|'''Script Library''']] — ''updated!''
|| [[: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="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="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]]'''
|}
|}


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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"
{| class="jtable" style="float: left; width: 90%;"
|+ 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="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
|-
| style="padding: 2px 5px 0px 15px;"| ♦ '''PyMOL now integrates seamlessly with MS Powerpoint.  See [[Axpymol]].'''
|-
| style="padding: 2px 5px 0px 15px;"| ♦ PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[group]] command has been added.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ The truly awesome [[grid_mode]] setting has been added.
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[Ellipsoids]] representation added for drawing thermal ellipsoids.
! New Setup
|}
| [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]].
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Caver.png|125px]] Screenshot of [[Caver]] showing cavities.
|}
|-
|-
|
! New Plugin
{|style="background-color: transparent;" width="100%"
| [[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.
|-
|-
|valign="top"|
! Official Release
{|style="background-color: transparent;" width="100%"
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts & Plugins
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[FindSeq]] — Find sequence or regular expression of amino acids in a protein.
! 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 10px 15px;"| ♦ [[Modevectors]] — creates arrow plots for normal mode analysis (NMA), NMR ensembles and other cases where you want to point out differences between similar objects.
! Official Release
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[GetNamesInSel]] — find the names of all objects in a selection.
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[CalcArea]] — find the area of any given object/selection;
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[ConnectedCloud]] — find connected clouds of objects 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;"| ♦ [[MakeVinaCommand]] — Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.
! 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;"| ♦ [[DrawBoundingBox]] — Draw a bounding box around your selection.
! 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;"| ♦ Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ Ever wanted to load all the PDBs in a directory within PyMOL?  Now you can load all files in a dir with [[LoadDir]].
! Older News
|-
| See [[Older_News|Older News]].
| style="padding: 2px 5px 0px 15px;"| ♦  [[PDB Web Services Script]] — Example using PyMOL and the PDB Web Services.
|-
| style="padding: 2px 5px 0px 15px;"| ♦  [[LigAlign]] — Ligand-based active site alignment and comparison.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
|}
|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:DrawMinBB.png|165px]] Screenshot of [[DrawBoundingBox]] in action.
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{| class="jtable" style="float: right; width: 90%"
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|+ 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; The Wiki experienced a few moments of downtime due to system maintenance. The downtime was <10 minutes.
|-
|-
| 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" >
|-
<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.
randomcount=1
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category=Commands|Plugins|Script_Library|Settings
| style="padding: 2px 5px 0px 15px;"| &diams; We got our '''2,000,000th''' page view!
includepage=*
|-
includemaxlength=1050
| style="padding: 2px 5px 0px 15px;"| &diams; Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests.
escapelinks=false
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allowcachedresults=false
| style="padding: 2px 5px 0px 15px;"| &diams; 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).
resultsheader=__NOTOC__ __NOEDITSECTION__
|-
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
| style="padding: 2px 5px 0px 15px;"| &diams; New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.
</DynamicPageList>
|}
</div>
|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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<DynamicPageList>
imagecontainer=Covers
randomcount=1
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listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
ordermethod=none
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Latest revision as of 13:01, 21 January 2025

hosted by SBGridlogo2.jpg
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
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...

Set name

set_name can be used to change the name of an object or selection.

Not only can you simply rename an object or selection, but this command is also a powerful tool for those who deal with multiple structures in one file --- say a collection of NMR models. The user can execute the Split_States command and then rename the molecule of choice in the state of choice. For example, if one loads an NMR structure (with, say, 20 states) and aligns it to another structure, the balance of the alignment will (most likely) be off due to the weighting of the 19 other structures you probably don't see. To overcome this problem, one simply executes Split_States and then renames one of the states and then aligns that newly renamed object.

USAGE

set_name old_name, new_name

PYMOL API

cmd.set_name(string old_name, string new_name)


User Comments/Examples

cmd.set_name("example", "nicename")

As the order of arguments is different from, for example, the ..→

A Random PyMOL-generated Cover. See Covers.


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