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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
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| 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]] <font color='red'><b>!</b></font>
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
|| [[:Category:Commands|Commands]]
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
|| '''Settings''': [[Settings|All]] | [[:Category:Settings|Documented]]
||'''[[PyMOL_mailing_list|Getting Help]]'''
|-
| [[:Category:Script_Library|'''Script Library''']] <font color='red'><b>!</b></font>
|| [[: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]
|-
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<!--
[http://www.pymol.org/ PyMOL 1.2] has been released! -->
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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"
 
|+ 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]])
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{|style="background-color: transparent;" width="100%"
{| class="jtable" style="float: left; width: 90%;"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
|-
|-
|valign="top"|
! Official Release
{|style="background-color: transparent;" width="100%"
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|-
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | 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;"| &diams; PyMOL is known to work under Mac OS X 10.6 (Snow Leopard) using the new Fink.  See [[MAC_Install#PyMOL_Install_from_Source.2C_Using_Fink|Installing PyMOL under Fink]].
! Official Release
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|-
|-
| style="padding: 2px 5px 0px 15px;"| &diams; PyMOL now has a [[Set]] command for basic settings, and a [[Set_bond]] command for bond-only settings.
! Python 3
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|-
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[Space]]&mdash; new command to control PyMOL's usage of color spaces.
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[CGOCylinder]]&mdash; information on CGO cylinders and circles in PyMOL.
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
| style="padding: 2px 5px 0px 15px;"| &diams; '''[http://www.pymol.org/ PyMOL] 1.2 is out!
! 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;"| &diams; Check out the artist who integrates PyMOL into [http://winkleman.com/artist/seriesview/1406/376 his work].
! 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;"| &diams; If you use the sequence viewer alot, or have lots of openGL text on the screen, try boosting your performance with [[Texture_fonts]].
! 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;"| &diams; '''PyMOL now integrates seamlessly with MS Powerpoint.  See [[Axpymol]].'''
! New Script
|}
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Image_large.png|125px]] Another cover made with PyMOL.  See [[User:Mazen|image details]].
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|-
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! Older News
{|style="background-color: transparent;" width="100%"
| See [[Older_News|Older News]].
|-
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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;" | Scripts, Plugins &amp; Tutorials
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[CollapseSel]]&mdash; simple script to compress selection lists: eg. instead of i. 1+2+3+4+5 you get 1-5.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[SuperSym]]&mdash; incredible script for handling crystallographic symmetry operations.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[CgoCircle]]&mdash; draw CGO circles in PyMOL; surround objects or selections with circles.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[MovieSchool]] &mdash; PyMOL Wiki's Movie School.  Learn how to make movies in PyMOL!
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[alphaToAll]] &mdash; Expands your desired alpha-carbon property down to all atoms in the residue.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[interfaceResidues]] &mdash; Finds interface residues in a complex.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSurfaceResidues]] &mdash; Find and show (if you want) surface exposed resiues in PyMOL.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[ToGroup]] &mdash; Converts a multistate object into a group of single state objects.
|-
| style="padding: 2px 5px 0px 15px;"| &diams; [[FindSeq]] &mdash; Find sequence or regular expression of amino acids in a protein.
|-
| style="padding: 2px 5px 10px 15px;"| &diams; [[Modevectors]] &mdash; 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;"| &diams; [[Pucker]] &mdash; finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
|}
|}
|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:DrawMinBB.png|165px]] Screenshot of [[DrawBoundingBox]] in action.
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
category=Commands|Plugins|Script_Library|Settings
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includepage=*
| style="padding: 2px 5px 0px 15px;"| &diams; [[Label]]s page was thoroughly refurbished.
includemaxlength=1050
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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.
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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
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| 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>
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| style="padding: 2px 5px 0px 15px;"| &diams; We got our '''2,000,000th''' page view!
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|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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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...

Align

Two proteins after structure alignment

align performs a sequence alignment followed by a structural superposition, and then carries out zero or more cycles of refinement in order to reject structural outliers found during the fit. align does a good job on proteins with decent sequence similarity (identity >30%). For comparing proteins with lower sequence identity, the super and cealign commands perform better.

Usage

align mobile, target [, cutoff [, cycles
    [, gap [, extend [, max_gap [, object
    [, matrix [, mobile_state [, target_state
    [, quiet [, max_skip [, transform [, reset ]]]]]]]]]]]]]

Arguments

  • mobile = string: atom selection of mobile object
  • target = string: atom selection of target object
  • cutoff = float: outlier rejection cutoff in RMS {default: 2.0}
  • cycles = int: maximum number of outlier rejection cycles {default: 5}
  • gap, extend, max_gap: sequence alignment parameters
  • object = ..→
A Random PyMOL-generated Cover. See Covers.


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