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" 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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=== Helping ===
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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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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="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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* A wiki edit/user policy is needed.
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* Wiki schema/design/organization: Below you'll find the current layout design
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* Graphic design and CSS layout: We need logos, BG images and CSS layout
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{| class="jtable" style="float: left; width: 90%;"
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* Importing the email list content: We have (lots) of email to sift through, extract data from and import into the Wiki
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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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* Etc...
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|-
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! Official Release
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| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
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|-
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! New Plugin
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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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|-
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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 fellowship announced for 2022-2023]
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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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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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=== Editors Needed ===
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|}
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If you feel you have the time to help import data into the PyMol wiki, please email [[User:Tree|Tree]].
 
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We need your help.  So join today & happy editing!
 
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[[User:Tree|Tree]]
 
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== Section Layout ==
 
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Please do not ADD any content to the site yet.  Just Organize the following list as logically as possible.  Here's my first go at it.
 
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Please see [[:Category:Discussion|Discussion]] for more thoughts on the site organizaiton.
 
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=== Layout Schema ===
 
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# [[:Category:News|News]]
 
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## [[:Category:Discussion|Discussion]]
 
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## [[:Category:PyMOL Beta|The Bleeding Edge]]
 
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# [[Technical Issues]] (installation, hardware)
 
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## [[Installation]]
 
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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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# [[Using the GUI]]
 
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## [[Launching PyMOL]]
 
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### [[Command Line Options]]
 
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### [[Launching From a Script]]
 
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## [[Mouse Controls]]
 
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## [[Objects and Selections]]
 
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### [[Working with Objects]]
 
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### [[Working with Selections]]
 
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### [[Selector Quick Reference]]
 
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#### [[Single-word Selectors]]
 
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#### [[Property Selectors]]
 
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#### [[Selection Algebra]]
 
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#### [[Selection Macros]]
 
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### [[Representations]]
 
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#### [[Lines]]
 
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#### [[Sticks]]
 
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#### [[Cartoon]]
 
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#### [[Surface]]
 
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#### [[Mesh]]
 
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#### [[Spheres]]
 
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#### [[Dots]]
 
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### [[Color]]
 
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### [[Displaying biochemical properties]]
 
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## [[Display Settings]]
 
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## [[Stereo 3D Display]]
 
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### [[Hardware Options]]
 
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### [[Linux XFree86 Configuration]]
 
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## [[Scenes]]
 
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## [[Mouse Settings]]
 
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## [[Wizards]]
 
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## [[Plugins]]
 
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## [[Ray-tracing]]
 
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## [[Settings Reference (all settings and what they do)]]
 
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## [[Movies and Animations]]
 
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## [[Structure Alignment]]
 
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## [[Structure Alignment Editor]]
 
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# [[:Category:Commands|Command Language]]
 
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## [[PyMOL Command Script]]
 
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## [[PyMOL Python API]]
 
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# [[Advanced Issues]] (Ray tracing, settings)
 
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## [[Launching PyMOL (has been asked often)]]
 
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## [[Advanced Atom Selections]]
 
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## [[Modeling and editing structures.]]
 
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### [[Editing atoms]]
 
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### [[Molecular sculpting]]
 
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### [[Homology modeling]]
 
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## [[Image Manipulation]]
 
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### [[labels]]
 
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### [[Photoshop/GIMP]]
 
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### [[Stereo Figures]]
 
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### [[Creating publication-quality images HOWTO]]
 
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# [[Scripting]]
 
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## [[Example Scripts]]
 
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## [[Script Library]]
 
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# [[Plugins]]
 
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## [[List of Plugins]]
 
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## [[How to do electrostatics and energy minimization.]]
 
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### [[APBS Plugin]]
 
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## [[rtools Plugin]]
 
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## [[Tutorial on writing plugins]]
 
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## [[Others]]
 
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# [[High-level applications]] (Crystallography, NMR)
 
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## [[Crystallography Applications]]
 
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### [[Symmetry]]
 
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### [[Electron Density]]
 
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## [[NMR Applications]]
 
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### [[Working with a Family of Structures]]
 
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### [[Superimposition and RMSD]]
 
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### [[NMR Restraints Analysis]]
 
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# [[3rd Party Software]]
 
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## [[3rd Party Applications]]
 
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### [[Movies]]
 
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### [[Codecs]]
 
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# [[Python Integration]]
 
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# [[Using PyMol For Unintended Uses]] (OpenGL Object Renderer)
 
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## [[Arbitrary Graphics Objects]]
 
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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 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...

ShowLigandWaters

Type Python Script
Download
Author(s) Gianluca Tomasello
License CC BY-NC-SA


Introduction

This script detects waters molecules within a specified distance from the ligand.
Detected water molecules are shown as spheres.
Distances between water molecules and O or N atoms of ligand (potential H-bonds) are shown by dotted lines.
An output file containing a list of distance between waters and ligand atoms and the number of interactions is written in the main PyMol folder.


Usage

waters [ligand name, distance]


Required Arguments

  • ligand name = the ligand residue name
  • distance = max distance in Angstroms


Examples

example #1 on PDB structure (1C0L) 

PyMOL>waters FAD, 2.8

Output in GUI of PyMol:

Total number of water molecules at 2.8 A from ligand FAD: 3 Number of water molecules that interact with ligand: 3 Number of interactions ..→

A Random PyMOL-generated Cover. See Covers.


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