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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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|+ 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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| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
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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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*** [Linux]
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! Official Release
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*** [MAC]
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
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*** [Windows]
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|-
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*** [[Script Library]]
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! Python 3
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
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* [[NMR Applicaitons]] (Doug Kojetin)
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|-
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* [[Plugins/Modules]] (Doug Kojetin)
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! POSF
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** [[APBS Plugin]]
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
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* [[Plugins]] (Michael George Werner)
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! Tutorial
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** [[List of Plugins]]
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| [[Plugins Tutorial]] updated for PyQt5
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** [[Tutorial on writing plugins]]
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** [[Others]]
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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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* [[Structure Alignment]] (Nat Echols)
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** [[Structure Alignment Editor]]
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! Selection keywords
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* [[3rd Party Applications]]
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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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** [[Movies]]
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** [[Codecs]]
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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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! 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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! Older News
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| See [[Older_News|Older News]].
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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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02:06, 16 Feb 2005 (CST)
 
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Latest revision as of 03:21, 22 June 2021

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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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