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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]]!
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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]]
|| [[: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="background-color: transparent;" width="100%"
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
|-
| style="padding: 2px 5px 0px 15px;"| ♦ '''[[http://www.pymol.org/ PyMOL]] 1.2 is out!
|-
| style="padding: 2px 5px 0px 15px;"| ♦ Check out the artist who integrates PyMOL into [http://winkleman.com/artist/seriesview/1406/376 his work].
|-
| style="padding: 2px 5px 0px 15px;"| ♦ If you use the sequence viewer alot, or have lots of openGL text on the screen, try boosting your performance with [[Texture_fonts]].
|-
| 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.
|}
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Image_large.png|125px]] Screenshot of [[Caver]] showing cavities.
|}
|-
|
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|-
|valign="top"|
{|style="background-color: transparent;" width="100%"
! 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;"| ♦ [[alphaToAll]] — Expands your desired alpha-carbon property down to all atoms in the residue.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[interfaceResidues]] — Finds interface residues in a complex.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[FindSurfaceResidues]] — Find and show (if you want) surface exposed resiues in PyMOL.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[ToGroup]] — Converts a multistate object into a group of single state objects.
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[FindSeq]] — Find sequence or regular expression of amino acids in a protein.
|-
| 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.
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
! Official Release
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[GetNamesInSel]] — find the names of all objects in a selection.
! 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;"| ♦ [[CalcArea]] — find the area of any given object/selection;
! Official Release
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[ConnectedCloud]] — find connected clouds of objects in PyMOL.
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
| 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.
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[DrawBoundingBox]] — Draw a bounding box around your selection.
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
! 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;"| ♦ Ever wanted to load all the PDBs in a directory within PyMOL?  Now you can load all files in a dir with [[LoadDir]].
! 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;"| ♦  [[PDB Web Services Script]] — Example using PyMOL and the PDB Web Services.
! 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;"| ♦  [[LigAlign]] — Ligand-based active site alignment and comparison.
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
! Older News
| See [[Older_News|Older News]].
|}
|}
|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:DrawMinBB.png|165px]] Screenshot of [[DrawBoundingBox]] in action.
|style="vertical-align: top; width: 40%"|
|}
{| 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...
|-
|-
|valign="top"|
|<div class="didyouknow" >
{|style="background-color: transparent;" width="100%"
<DynamicPageList>
|-
randomcount=1
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
category=Commands|Plugins|Script_Library|Settings
|-
includepage=*
| style="padding: 2px 5px 0px 15px;"| &diams; [[Label]]s page was thoroughly refurbished.
includemaxlength=1050
|-
escapelinks=false
| style="padding: 2px 5px 0px 15px;"| &diams; The Wiki experienced a few moments of downtime due to system maintenance.  The downtime was <10 minutes.
allowcachedresults=false
|-
resultsheader=__NOTOC__ __NOEDITSECTION__
| 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.
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
|-
</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.
</div>
|-
<div style="clear: both;"></div>
| style="padding: 2px 5px 0px 15px;"| &diams; We got our '''2,000,000th''' page view!
|-
| style="padding: 2px 5px 0px 15px;"| &diams; Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests.
|-
| 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).
|-
| style="padding: 2px 5px 0px 15px;"| &diams; New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.
|}
|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
escapelinks=false
openreferences=true
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
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allowcachedresults=false
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Latest revision as of 11:54, 12 March 2024

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
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...

Pml2py

This script converts a pml script to a python script.

See pymol-users mailing list (Subject: Convert pml script to Pymol Python script, Fri, 8 Apr 2011).

<source lang="python"> from __future__ import print_function

import sys from pymol import cmd, parsing

def pml2py(filename, out=sys.stdout):

DESCRIPTION 

   Convert a pml script to python syntax.

USAGE 

   pml2py infile [, outfile]
   
   def quote(args):
       args = iter(args)
       for arg in args:
           if '=' not in arg:
               prefix = 
           else:
               prefix, arg = arg.split('=', 1)
               prefix += '='
               arg = arg.lstrip()
           yield prefix + repr(arg)

   class stackiter:
       def __init__(self, collection):
           self.iterator = iter(collection)
           self.stack = []
       def __iter__(self):
           return self
       def next(self):
           if len(self.stack):
               return  ..→
A Random PyMOL-generated Cover. See Covers.


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