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== PyMol Wiki Home ==
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__NOTOC__
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You have reached the 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: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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We provide
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* updates on [http://pymol.sf.net PyMol]
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* a stable user-oriented documentation base
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* a thorough treatment of the PyMol program
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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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* feature-rich scripts for general PyMol use
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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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| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
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||'''[[PyMOL_mailing_list|Getting Help]]'''
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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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| 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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|-
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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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{| 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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imagecontainer=Covers
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==News==
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|}
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* Pymol 0.99 is out! Get it [http://delsci.com/rel/099/ here].
 
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* [[APBS]] page established.  A new version of APBS plugin is provided.
 
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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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* New cool [[ray]] tracing features added!
 
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* New [http://www.delsci.com/beta Beta Releases] available.
 
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* New PyMol Features: [[Examples_of_cartoon_ring_and_cartoon_ladder_settings|Nucleic Acid Representation Settings]] & Examples.
 
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* Cool new Plug-In: [[Show_NMR_constrains| Show NMR Constrains]].
 
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* Check out PyMol's new [[Cartoon#Nucleic_Acid_Representation|Nucleic Acid Rendering]]
 
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* Added [[DynoPlot]] script for plotting data within PyMol; an interactive Ramachandran plot.
 
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* Added [[Kabsch]] script for optimal alignment of two sets of vectors.
 
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* Some details have been released about [[0.99beta11]]'s release and new features.
 
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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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* [[:Special:Allpages| All Pages]]
 
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* [[:Category:Plugins|Plugins]]
 
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* [[:Special:Categories| See All Categories]]
 

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...

Intra fit

intra_fit fits all states of an object to an atom selection in the specified state. It returns the rms values to python as an array.

USAGE

intra_fit (selection),state

PYMOL API

cmd.intra_fit( string selection, int state )

EXAMPLES

Simple Selection

intra_fit ( name ca )

Fitting NMR Ensembles

Warren provided a great example on the PyMOL list. If the NMR ensemble has all the structures loaded as multiple states (which is the default behavoir (see split_states) for multimodel PDBs) then we can simply call: 

print cmd.intra_fit(selection, state)

which will fit all of the other states to the indicated states and return the RMS values as a list.

A simple example is: <source lang="python"> fetch 1i8e, async=0 print cmd.intra_fit("1i8e////CA", 1)

  1. ..→
A Random PyMOL-generated Cover. See Covers.


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