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* [[TOPTOC|'''Table of Contents''']]
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* [[Special:Allpages|Alphabetized Index of all pages]]
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<br>
{| 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!
|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
| 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;"
| 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;"
|}


== PyMol Wiki Home ==
{| 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;"
You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.
|+ 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
|-
| 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]]'''
|-
| 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]]'''
|}


We provide
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* updates on [http://pymol.sf.net PyMol]
| style="vertical-align: top; width: 40%" |
* a stable user-oriented documentation base
{| class="jtable" style="float: left; width: 90%;"
* a thorough treatment of the PyMol program
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
* feature-rich scripts for general PyMol use
|-
! 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]].
|-
! 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.
|-
! Official Release
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
! 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
|-
! Official Release
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
! New Plugin
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
! Selection keywords
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
! 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
|-
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
! Older News
| See [[Older_News|Older News]].
|}
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{| 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...
|-
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== New Users ==
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The PyMol Wiki actively seeks new users and contributors!  However, due to massive amount of spamming, we've changed the registration process, until further notice.  '''If you would like access,''' you will need to be verified by a system administrator/sysop.  To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol).  Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''.  Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.
 
==News==
===PyMol===
* Added a page that lists all [[Settings|PyMol settings]].  We need to stat documenting these.
* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
* A new version of APBS plugin is available on [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page].
* New [http://www.delsci.com/beta Beta Releases] available.
 
===Wiki===
* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
* [[APBS]] page has been established. 
* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
* New cool [[ray]] tracing features added!
 
===News Archive===
*See our [[Older_News]].
 
== Links of Interest ==
* [[TOPTOC|Top Level Table of Contents]]
* [[:Category:FAQ|Frequently Asked Questions]] -- new!
* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
* [[:Category:Commands|PyMol Commands]] (>130 documented!)
* [[:Special:Allpages| All Pages]]
* [[:Category:Plugins|Plugins]]
* [[:Special:Categories| See All Categories]]

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...

Wfmesh

Type Python Script
Download wfmesh.py
Author(s) Dan Kulp
License -
This code has been put under version control in the project Pymol-script-repo

DESCRIPTION

This script will create an object for any Wavefront(.OBJ) mesh file. This is a way to extend the number of objects you can use. Also, you have more control over the coloring, transformations, etc than the CGOs. Although there are a number of these obj files on the web, you can also easily created them with open source tools (OpenFX, Crossroads3D). It takes literally, 2 min to get an object created and then loaded into pymol. Simply open OpenFX Designer, click File->Insert->Model, then choose any of the models (or create your own of course!), then export it as .3ds file. Then open the .3ds file from Crossroads3D and export as Wavefront OBJ.

  • createWFMesh - create a mesh object from Wavefront (*.obj) formated file

IMAGES

Star Wars Anyone?
..→
A Random PyMOL-generated Cover. See Covers.


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