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* [[TOPTOC|'''Table of Contents''']]
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* [[Special:Allpages|Alphabetized Index of all pages]]
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* [[Improvements|Discussion of PyMolWiki Improvements]]
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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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You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.
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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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| 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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||'''[[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 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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== 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''', 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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* If you notice something out of the ordinary, please contact the admin.  I updated some software.
 
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* [[Slerpy]], a set of pymol command extensions to simplify complex movie making is now available.
 
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* Updated the [[Kabsch#The_New_Code|Kabsch]] code with a more elegant solution; fixed a small rotation bug.
 
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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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* [[Settings]] now contains documentation on:
 
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              - helix roundness
 
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              - ribbon sampling
 
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              - cartoon sampling
 
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              - cartoon highlight coloring
 
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              - cartoon color blending vs discrete colors
 
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              - and more!  now 48 documented (with examples); just 470 to go....
 
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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]]  (6 newly documented; only 470 to go...)
 
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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...

FilterByMol

== Overview ==

This script filters through all the PDBs in the parent dir (you can easily the the directory it scans). For each molecule, it saves just the ligands/heteroatoms (excluding the waters). This gives you a simple way to filter through a database of proteins looking only at their ligands.

This script, as noted below, works on the objects at the level of a molecule. While we can iterate over atom number (ID), residue number (resi), etc we do not have any such "MOLID". So, we provide this simple workaround. You might need this file because if you have a residue (like #111 from 3BEP) that consists of a molecule and an atom then there's no other way to save the separate pieces (of molecule/atom) into two (or more files). As you can see in the following listing, if we iterate over the hetero atoms (and not waters) in 3BEP we get, <source lang="python"> PyMOL>iterate bymol het, print resi, resn, ID, chain, segi, alt 111 5CY 6473 C 111 5CY 6474 C 111 5CY 6476 C 111 5CY 6477 C 111 5CY 6478 C 111 5CY ..→

A Random PyMOL-generated Cover. See Covers.


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