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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
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| We are the community-based support site for the popular molecular visualization program, [http://pymol.sf.net PyMOL].
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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!
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! 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.
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! 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
|-
| 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]]'''
|-
|-
| [[TOPTOC|'''Table of Contents''']]
| 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]]'''
|| [[Special:Allpages|Index of all pages]]
|| '''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;"|'''[[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%"
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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;"| ♦ 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;"| ♦ [[interfaceResidues]] — Finds interface residues in a complex.
! Official Release
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[FindSurfaceResidues]] — Find and show (if you want) surface exposed resiues in PyMOL.
! 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;"| ♦ [[ToGroup]] — Converts a multistate object into a group of single state objects.
! Official Release
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[FindSeq]] — Find sequence or regular expression of amino acids in a protein.
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
| 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.
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[GetNamesInSel]] — find the names of all objects in a selection.
! 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;"| ♦ [[CalcArea]] — find the area of any given object/selection;
! 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;"| ♦ [[ConnectedCloud]] — find connected clouds of objects in PyMOL.
! 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;"| ♦ [[MakeVinaCommand]] — Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
| style="padding: 2px 5px 0px 15px;"| ♦ [[DrawBoundingBox]] — Draw a bounding box around your selection.
! Older News
|-
| See [[Older_News|Older News]].
| style="padding: 2px 5px 0px 15px;"| ♦ Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
|-
| 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]].
|-
| 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.
|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...
|-
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{|style="background-color: transparent;" width="100%"
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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;"| ♦ [[Label]]s page was thoroughly refurbished.
|-
| 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.
|-
|-
| 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 class="didyouknow" >
|-
<DynamicPageList>
| style="padding: 2px 5px 0px 15px;"| &diams; We got our '''2,000,000th''' page view!
randomcount=1
|-
category=Commands|Plugins|Script_Library|Settings
| style="padding: 2px 5px 0px 15px;"| &diams; Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests.
includepage=*
|-
includemaxlength=1050
| 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).
escapelinks=false
|-
allowcachedresults=false
| style="padding: 2px 5px 0px 15px;"| &diams; New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.
resultsheader=__NOTOC__ __NOEDITSECTION__
|}
listseparators=,<h3>[[%PAGE%]]</h3>,,\n
|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:Science090410.jpg|125px]] Sample Cover from the [[Covers]] gallery.
</DynamicPageList>
</div>
<div style="clear: both;"></div>
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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
ordermethod=none
allowcachedresults=false
</DynamicPageList>
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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...

Grepsel

Create selections matching motifs, using python regular expression syntax.

This is very similar to the FindSeq script.

The Code

<source lang="python">

  1. Create named selections using regular expressions for the protein sequence

import pymol import re cmd = pymol.cmd

aa = { 'ASP' : 'D' , 'GLU' : 'E' , 'GLN' : 'Q' , 'ASN' : 'N' , 'SER' : 'S' , 

      'THR' : 'T' , 'CYS' : 'C' , 'HIS' : 'H' , 'ARG' : 'R' , 'LYS' : 'K' ,
      'MET' : 'M' , 'ALA' : 'A' , 'ILE' : 'I' , 'LEU' : 'L' , 'VAL' : 'V' ,
      'GLY' : 'G' , 'PRO' : 'P' , 'TRP' : 'W' , 'PHE' : 'F' , 'TYR' : 'Y' ,
      'SCY' : 'U' , 'ASX' : 'B' , 'GLX' : 'Z' , 'XXX' : 'X'}
  1. made this before the sequence view option, probably another way to do it now

def seqoneint(model): 

  pymol.stored.seq = []
  cmd.iterate("%s and name ca"%model,"stored.seq.append(resn)")
  seq = ""
  for x in pymol.stored.seq:
     if aa.has_key(x):
        res = aa[x]
        seq = seq+res
     else:
        seq = seq + '-'
  return seq


def grepsel(selection="(all)",stretch="",pr ..→

A Random PyMOL-generated Cover. See Covers.


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