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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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== Moving In ==
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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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Please excuse the mess as we create the PyMolWiki site. The wiki will be a valuable educational & reference tool for PyMol users.
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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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== Helping ==
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{| width="100%"
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If you feel like helping out, please login and get to work. :-) For design/layout purposes you must be logged in to edit pages.  We now need people to assist with
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| style="vertical-align: top; width: 40%" |
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{| class="jtable" style="float: left; width: 90%;"
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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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|-
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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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! 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 fellows announced for 2018-2019]
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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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</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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* Wiki schema/design/organization
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|}
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* Graphic design and CSS layout
 
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* Importing the email list content
 
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* Smoothing out the edges
 
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* Etc...
 
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We need your help.  So join today & happy editing!
 
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~~
 
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== [[Initial Wiki Layout Suggestion]] == (Warren Delano)
 
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* [[Mouse Controls]]
 
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* [[Command Language]]
 
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* [[Atom Selections]]
 
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* [[Ray-tracing]]
 
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* [[Movies and Animations]]
 
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* [[Cartoon Representations]]
 
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* [[Settings Reference (all settings and what they do)]]
 
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* [[Stereo 3D Display]]
 
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** [[Hardware Options]]
 
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** [[Linux XFree86 Configuration]]
 
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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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* [[Installation]] ([[User:Tree|Tree]])
 
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** [[Hardware Requirements]]
 
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** [[Software Requirements]]
 
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** [[OS Dependent]]
 
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*** [[Linux]]
 
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*** [[MAC]]
 
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*** [[Windows]]
 
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*** [[Script Library]]
 
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* [[NMR Applicaitons]] (Doug Kojetin)
 
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* [[Plugins/Modules]] (Doug Kojetin)
 
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** [[APBS Plugin]]
 
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* [[Plugins]] (Michael George Werner)
 
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** [[List of Plugins]]
 
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** [[Tutorial on writing plugins]]
 
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** [[Others]]
 
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* [[Structure Alignment]] (Nat Echols)
 
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** [[Structure Alignment Editor]]
 
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* [[3rd Party Applications]]
 
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** [[Movies]]
 
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** [[Codecs]]
 
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* [[Displaying biochemical properties]] (Kristian Rother)
 
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* [[Coloring molecules]]
 
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* [[Rendering molecules]]
 
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** [["basics of displaying molecules".]]
 
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** [["displaying basic chemical properties", like double bonds, h-bonds, bond angles and b-factors.]]
 
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* [[Modeling and editing structures. ]]
 
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* [[How to do electrostatics and energy minimization.]]
 
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* [[Launching PyMOL (has been asked often)]]
 
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* [[Some kind of "script collection" would be very useful.]]
 
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----
 
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[[User:Tree|Tree]] 02:09, 16 Feb 2005 (CST)
 
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----
 

Latest revision as of 03:21, 22 June 2021

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 v2.5 has been released on May 10, 2021.
Python 3 New Python 3 compatibility guide for scripts and plugins
POSF New PyMOL fellows announced for 2018-2019
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...

Super

super aligns two selections.

It does a sequence-independent (unlike align) structure-based dynamic programming alignment followed by a series of refinement cycles intended to improve the fit by eliminating pairing with high relative variability (just like align). super is more robust than align for proteins with low sequence similarity.

Usage

See align command.

Caveats

  • Alternative Conformations: If super ever tells you no matched atoms, then instead of 
    super p1, p2
    try 
    super p1 & alt A+'', p2 & alt B+''

User Scripts

Write rmsd to file

pymol_rmsd_test.pml 

reinitialize

fetch 1F9J, async=0
fetch 1YX5, async=0

extract 1F9J_A, 1F9J and chain A
extract 1YX5_B, 1YX5 and chain B

test=cmd.super("1F9J_A","1YX5_B")

python
writefile=open("rmsd_file.txt","a")
writefile.write(' '.join('%s' % x for x in test))
writefile.write('\n')
writefile.close()
python end

In ..→

A Random PyMOL-generated Cover. See Covers.


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