Difference between revisions of "Main Page"

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== PyMol Wiki Home ==
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__NOTOC__
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You have reached the (new) home of the PyMolWiki, a user-driven web-oriented CMS.
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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;"
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|+ 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/]]
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|}
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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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== [[Initial Wiki Layout Suggestion]] == (Warren Delano)
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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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* [[Mouse Controls]]
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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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* [[Command Language]]
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|-
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* [[Atom Selections]]
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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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* [[Ray-tracing]]
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|-
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* [[Movies and Animations]]
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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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* [[Cartoon Representations]]
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|-
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* [[Settings Reference (all settings and what they do)]]
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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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* [[Stereo 3D Display]]
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||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
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** [[Hardware Options]]
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||'''[[PyMOL_mailing_list|Getting Help]]'''
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** [[Linux XFree86 Configuration]]
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|}
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* [[Crystallography Aplications]]
 
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** [[Symmetry]]
 
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** [[Electron Density]]
 
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* [[Arbitrary Graphics Objects]]
 
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* [[Python Integration]]
 
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* [[Scenes]]
 
  
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== [[User Additions]] ==
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{| width="100%"
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* [[Installation]] ([[User:Tree|Tree]])
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| style="vertical-align: top; width: 40%" |
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** [[Hardware Requirements]]
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{| class="jtable" style="float: left; width: 90%;"
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** [[Software Requirements]]
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
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** [[OS Dependent]]
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|-
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*** [Linux]
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! Official Release
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*** [MAC]
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| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
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*** [Windows]
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|-
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*** [[Script Library]]
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! New Plugin
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----
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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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* [[NMR Applicaitons]] (Doug Kojetin)
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|-
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* [[Plugins/Modules]] (Doug Kojetin)
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! Official Release
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** [[APBS Plugin]]
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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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|-
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* [[Plugins]] (Michael George Werner)
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! Python 3
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** [[List of Plugins]]
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
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** [[Tutorial on writing plugins]]
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|-
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** [[Others]]
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! POSF
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| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
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* [[Structure Alignment]] (Nat Echols)
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|-
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** [[Structure Alignment Editor]]
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! Tutorial
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* [[3rd Party Applications]]
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| [[Plugins Tutorial]] updated for PyQt5
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** [[Movies]]
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|-
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** [[Codecs]]
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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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category=Commands|Plugins|Script_Library|Settings
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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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</div>
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<div style="clear: both;"></div>
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|}
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|style="vertical-align: top; width: 18%"|
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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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02:06, 16 Feb 2005 (CST)
 
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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.


Retrieved from "http://pymolwiki.org/index.php?title=Main_Page&oldid=13571"