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__NOTOC__
__NOTOC__
{| align="center" style="padding-bottom: 4em;"
{| 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:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | 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: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
|}
{| 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.
| 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;"
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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;"
 
|+ 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
{| 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
|-  
|-  
| style="font-size: 1.1em; color #61021F; 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:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
|-
|-
| 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]]'''
| 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; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
| 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]]'')
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[GoogleSearch]]'''
||'''[[PyMOL_mailing_list|Getting Help]]'''
|}
|}


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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|-
|-
! Schrodinger Buys PyMOL
! New Setup
| Schrodinger has purchased PyMOL. Development, support and open-source fun to continue!  Read about the [http://www.schrodinger.com/News.php?mID=7&sID=6&cID=253 sale].
| [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]].
|-
! User Movie
| One of our users has posted another [[http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie]], images from which were created with PyMOL.
|-
|-
! New setting
! New Plugin
| [[surface_cavity_mode]] to change how PyMOL displays cavities.
| [[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.
|-
|-
! Search fixed.
! Official Release
| Thanks to a eagle-eyed user, our search has been fixed.  Please let us know if you have any search-related problems.
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
|-
! New Command
! New Plugin
| [[Cache]]—stores information on structures, so we don't have to recompute them.
| [[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
|-
|-
! Warren
! Official Release
| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
|-
! Setting
! Python 3
| [[Fetch_Path]]—Sets the default path for the [[fetch]] command.
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
! New Script
! POSF
| [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box.
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
! New Script
! Tutorial
| [[ContactsNCONT]]—The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
! Fun
! New Plugin
| [http://www.youtube.com/watch?v=oCRJ4r0RDC4 PCR Rap] video made with PyMOL (YouTube).
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
|-
! PyMOLWiki
! Selection keywords
| Reformatted Main Page. Some delays might occur from resizing images, but that should go away once the images are cached.
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
|-
! PyMOLWiki
! Plugin Update
| New — Search the PyMOLWiki via [[GoogleSearch]]
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
|-
|-
! PyMOL
! New Script
| 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]].
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
! PyMOL
! Older News
| PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
| See [[Older_News|Older News]].
|}
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Latest revision as of 12:01, 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...

SaveGroup

This script creates the command "saveGroup". saveGroup will save the specified group to disk as one file with all group objects in it, or as many files one pdb in each file. To save to one file just call 
saveGroup groupName
to save to many files call 
saveGroup groupName, oneFile=False
.

The Code

<source lang="python"> import pymol from pymol import cmd, stored


def saveGroup(g, oneFile=None): 

   """
   Save all files inside group 'g' to either
   one file or a list of files
   
   PARAMS
   g
       name of the group to save

   oneFile
       if not specified or None, saves each protein in the group
       to its own file, if oneFile=True, then saves all the files
       in the group to just one file.
       
   RETURNS
       None
   """

   oneFile = (oneFile!=None)

   if cmd.get_type(g) != "object:group":
       print "Error: please provide a group name to save."
       return

   stored.models = set()
   cmd.iterate(g, 'stored.models.ad ..→
A Random PyMOL-generated Cover. See Covers.


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