Difference between revisions of "Main Page"

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(Added PyMol Settings to the Links of Interest so it's still around when it get's bumped off the news)
(PyMOL 3.0 release)
 
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* [[TOPTOC|'''Table of Contents''']]
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* [[Special:Allpages|Alphabetized Index of all pages]]
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{| 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!
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|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
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| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
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|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
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| To request a new account, email SBGrid at: accounts (@) sbgrid dot org
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|- style="text-align:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
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|}
  
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== PyMol Wiki Home ==
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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;"
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You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.
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|+ 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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|-
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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]]'''
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|-
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| 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]]'''
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|-
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| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
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||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
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||'''[[PyMOL_mailing_list|Getting Help]]'''
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|}
  
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We provide
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* updates on [http://pymol.sf.net PyMol]
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| style="vertical-align: top; width: 40%" |
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* a stable user-oriented documentation base
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{| class="jtable" style="float: left; width: 90%;"
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* a thorough treatment of the PyMol program
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
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* feature-rich scripts for general PyMol use
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|-
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! Official Release
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| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
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|-
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! New Plugin
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| [[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
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|-
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! Official Release
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
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|-
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! Python 3
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
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|-
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! POSF
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| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
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|-
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! Tutorial
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| [[Plugins Tutorial]] updated for PyQt5
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|-
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! New Plugin
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| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
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|-
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! Selection keywords
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| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
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|-
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! Plugin Update
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
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|-
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! New Script
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| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
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|-
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! Older News
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| See [[Older_News|Older News]].
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|}
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|style="vertical-align: top; width: 40%"|
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{| class="jtable" style="float: right; width: 90%"
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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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|-
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|<div class="didyouknow" >
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<DynamicPageList>
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randomcount=1
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category=Commands|Plugins|Script_Library|Settings
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includepage=*
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includemaxlength=1050
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escapelinks=false
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allowcachedresults=false
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resultsheader=__NOTOC__ __NOEDITSECTION__
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listseparators=,<h3>[[%PAGE%]]</h3>,,\n
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<DynamicPageList>
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imagecontainer=Covers
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randomcount=1
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escapelinks=false
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openreferences=true
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listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
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ordermethod=none
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allowcachedresults=false
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</DynamicPageList>
  
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== New Users ==
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The PyMol Wiki actively seeks new users and contributors!  However, due to massive amount of spamming, we've changed the registration process, until further notice.  '''If you would like access,''' you will need to be verified by a system administrator/sysop.  To do so, email Jason dot Vertrees at gmail dot com (and tell me why you use PyMol).  Also, be sure to include your '''desired user name''', '''real name''', '''temporary password''', and '''email address'''.  Once we figure out a way to automatically prevent spamming, we'll return to the normal method of registration.
 
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==News==
 
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===PyMol===
 
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* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
 
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* A new version of APBS plugin is available on [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page].
 
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* New [http://www.delsci.com/beta Beta Releases] available.
 
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* New cool [[ray]] tracing features added!
 
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===Wiki===
 
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* [[SURFNET]] information on reading surfaces from other programs added.
 
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* Two new [[:Category:Plugins|Plugins]] have been added, [[NsSNP Loader]] and [[Proxy Config]].
 
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* Added a page that lists all [[Settings|PyMol settings]].  We need to start documenting these.
 
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* [[MAC_Install]] page has been developed. It describes pymol and apbs issues specific to Mac OS X.
 
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* [[APBS]] page has been established. 
 
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* [[APBS]] How to set this up on OS X and on Linux has been started but needs contributions.
 
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===News Archive===
 
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*See our [[Older_News]].
 
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== Links of Interest ==
 
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* [[TOPTOC|Top Level Table of Contents]]
 
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* [[:Category:FAQ|Frequently Asked Questions]] -- new!
 
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* [[PyMolWiki:Community_Portal| How to get involved!]] -- read me if you want to add something
 
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* [[:Category:Script Library| Script Library]] -- add one! (rTools info!)
 
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* [[:Category:Commands|PyMol Commands]] (>130 documented!)
 
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* [[Settings|PyMol Settings]]
 
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* [[:Special:Allpages| All Pages]]
 
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* [[:Category:Plugins|Plugins]]
 
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* [[:Special:Categories| See All Categories]]
 

Latest revision as of 12:54, 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...

LigAlign

===IMAGES===

  • Ligand-based alignment of 1XBB and 1OPJ

  • Atom-to-atom mapping of ligands

  • Alignment of 1V07 and 1HBI using heme

DESCRIPTION

LigAlign is a tool to compare protein active-sites and investigate ligand binding. The active-site alignment is guided by the orientation of bound ligands in the protein active sites. LigAlign supports analysis of flexible ligand via automatic fragment-based alignment: first computing a natural fragmentation of the query ligand, aligning each fragment of the query independently against the baseline, and then permitting easy visualization of each active site subcavity.

We use protein-ligand complexes to compare the active sites of several proteins which interact with a chosen ligand. Beginning with a user-specified protein-ligand structure, LigAlign gathers experimental structures of other proteins bound to the ligand from the Protein Data Bank. The tool then aligns the ligands bound in the ..→

A Random PyMOL-generated Cover. See Covers.


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