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__NOTOC__
__NOTOC__
{| align="center"
{| 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="width: 90%; 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="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;"
| 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="center" width="45%" style="background: #FFFFFF; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
{| align="center" style="width:90%; margin-bottom: 20px"
|+ 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
|
|-
{| align="left" width="20%" style="border: 1px solid #333; text-align:center; height=100%;"
| 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-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
|-
|-
| style="background:#E6EFFF; color:#333; font-size: 110%; padding: 4.5px"| New users are encouraged to join. Feel free to add any appropriate content; make an account and get started!
| 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]]'''
|}
|}
{| 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
{| 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 & Updates
|-
|-
| [[TOPTOC|'''Table of Contents''']]
! New Setup
|| [[Special:Allpages|Index of all pages]]
| [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]].
|| '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] [[CheatSheet|Wiki Page]]
|-
|-
| [[:Category:Tutorials|Tutorials]]
! New Plugin
|| [[:Category:Commands|Commands]]
| [[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.
|| '''Settings''': [[Settings|All]] [[:Category:Settings|Documented]]
|-
|-
| [[:Category:Script_Library|'''Script Library''']]
! Official Release
|| [[:Category:Plugins|'''Plugins''']]
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|| [[:Special:Categories| See All Categories]]
|-
|-
| [[:Category:FAQ|Frequently Asked Questions]]
! New Plugin
|| [[PyMolWiki:Community_Portal|'''How to get involved!''']]
| [[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
|| [[About| '''About PyMOL''']]
|-
|-
|}
! Official Release
|
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|}
 
{| 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"|
! Python 3
{|style="background-color: transparent;" width="100%"
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [http://www.google.com/analytics/ Google Analytics] cookies/tracking added to the wiki.  We're just doing hit counts and watching what people do so we can improve the wiki.
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[CheatSheet|PyMOL Cheat Sheet]] (reference card) has been donated.  It's also posted in the table above for quick access.
! New Plugin
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ '''[[Gsoc2008|Google Summer of Code 2008 for PyMOL]]''' has been created. '''Update:''' PyMOL wasn't chosen, so this page is now about ideas for improving PyMOL.
! 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: 3px 5px 10px 15px;"| ♦ Added a special category/section for active PyMOL [[:Category:Tutorials|Tutorials]]. These are pages not just with information, but easy to understand, step-by-step pages from which to learn.
! 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
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:refcard.png|155px]] Screenshot of the donated [[CheatSheet|PyMOL reference card]].
|}
|-
|-
|
! New Script
{|style="background-color: transparent;" width="100%"
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
|valign="top"|
! Older News
{|style="background-color: transparent;" width="100%"
| See [[Older_News|Older News]].
|}
|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...
|-
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
|<div class="didyouknow" >
|-
<DynamicPageList>
| style="padding: 3px 5px 10px 15px;"| &diams; [[group]] command has been added.
randomcount=1
|-
category=Commands|Plugins|Script_Library|Settings
| style="padding: 3px 5px 10px 15px;"| &diams; The truly awesome [[grid_mode]] setting has been added.
includepage=*
|-
includemaxlength=1050
| style="padding: 3px 5px 10px 15px;"| &diams; [[Ellipsoids]] representation added for drawing thermal ellipsoids.
escapelinks=false
|}
allowcachedresults=false
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Gm1.png|125px]] Screenshot of [[grid_mode|Grid Mode]] in action.
resultsheader=__NOTOC__ __NOEDITSECTION__
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
</DynamicPageList>
</div>
<div style="clear: both;"></div>
|}
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|-
|
|
{|style="background-color: transparent;" width="100%"
|style="vertical-align: top; width: 18%"|
|-
<DynamicPageList>
|valign="top"|
imagecontainer=Covers
{|style="background-color: transparent;" width="100%"
randomcount=1
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts &amp; Plugins
escapelinks=false
|-
openreferences=true
| style="padding: 3px 5px 10px 15px;"| &diams; [[ImmersiveViz]] -- Headtracking user interface for PyMOL  (watch the video)!
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
|-
ordermethod=none
| style="padding: 3px 5px 10px 15px;"| &diams; [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars
allowcachedresults=false
|-
</DynamicPageList>
| style="padding: 3px 5px 10px 15px;"| &diams; [http://ase-web.rit.edu/~ez-viz/ProMOL_dl.html ProMOL] plugin added.  Catalytic site prediction, other tools.  Redirects to website.
 
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[EMovie]] plugin added.  Easy movies in PyMol using a GUI.
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[DYNMAP]] plugin page created.  Check it out!
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[EZ-Viz]]
|}
|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:COLORAMA-screenshot.jpg|125px]] Screenshot of [[Colorama]].
|}
|}
|}

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...

SelInside

selInside selects all atoms of a certain type that are located within the bounding box defined by some selection. See examples.

Usage

# find all atoms inside the box spanned by (0,0,0) and (10,10,10)
# for the example PDB, 1hpv
fetch 1hpv
pseudoatom b1, pos=[0,0,0]
pseudoatom b2, pos=[10,10,10]
selInside b1 or b2


The Code

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

def selInside(bounding_object, target="*", radius=None): 

   """
   Selects all atoms of a given target type inside some selection that acts like a bounding box.

   PARAMS:
       bounding_object -- [PyMOL object/selection] the object/selection inside of which we want to choose atoms
       target -- [PyMOL selection] that defines the atoms to select.  Use "solvent" to select
                 only solvent atoms inside the selection
       radius -- [float] expand the box by this many angstroms on all sides

   RETURNS:
       (string) name of the selection created

  ..→
A Random PyMOL-generated Cover. See Covers.


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