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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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=== 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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{| width="100%"
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* Wiki schema/design/organization: Below you'll find the current layout design
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| style="vertical-align: top; width: 40%" |
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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 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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|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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=== 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:News Discussion|Discussion]]
 
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## [[:Category:News PyMol Beta|PyMol Beta]]
 
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# [[:Category:Technical Issues|Technical Issues]]
 
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## [[:Category:Technical Issues Installation|Installation]]
 
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### [[:Category:Technical Issues Installation OS Dependent|OS Dependent]]
 
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#### [[:Category:Technical Issues Installation OS Dependent Linux|Linux]]
 
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#### [[:Category:Technical Issues Installation OS Dependent MAC|MAC]]
 
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#### [[:Category:Technical Issues Installation OS Dependent Windows|Windows]]
 
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# [[:Category:Launching PyMOL|Launching PyMOL]]
 
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## [[:Category:Launching PyMOL Command Line Options| Command Line Options]]
 
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## [[:Category:Launching PyMOL Launching From a Script|Launching From a Script]]
 
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# [[Using the GUI]]
 
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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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## [[:Category:Commands PyMOL Command Script|PyMOL Command Script]]
 
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## [[:Category:Commands PyMOL Python API|PyMOL Python API]]
 
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# [[:Category:Advanced Issues|Advanced Issues]]
 
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## [[:Category:Advanced Issues Modeling and Editing Structures|Modeling and editing structures]]
 
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### [[:Category:Advanced Issues |Editing atoms|Editing Atoms]]
 
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### [[:Category:Advanced Issues Molecular Sculpting|Molecular sculpting]]
 
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### [[:Category:Advanced Issues Homology Modeling|Homology modeling]]
 
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## [[:Category:Advanced Issues Image Manipulation|Image Manipulation]]
 
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### [[:Category:Advanced Issues labels|labels]]
 
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### [[:Category:Advanced Issues Photoshop and GIMP|Photoshop/GIMP]]
 
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### [[:Category:Advanced Issues Stereo Figures|Stereo Figures]]
 
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### [[:Category:Advanced Issues Publication Quatlity Images|Publication-quality images]]
 
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# [[:Category:Scripting|Scripting]]
 
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## [[:Category:Scripting Example Scripts|Example Scripts]]
 
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## [[:Category:Scripting Script Library|Script Library]]
 
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# [[:Category:Plugins|Plugins]]
 
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## [[:Category:Plugins Electrostatics and Energy Minimization| How to do electrostatics and energy minimization.]]
 
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### [[:Category:Plugins APBS| APBS Plugin]]
 
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## [[:Category:Plugins rtools | rtools]]
 
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## [[:Category:Plugins Tutorial|Tutorial on writing plugins]]
 
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## [[:Category:Plugins Others| Others]]
 
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# [[:Category:High-Level Applications|High-Level Applications]] (Crystallography, NMR)
 
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## [[:Category:High-Level Applications Crystallography Applications|Crystallography Applications]]
 
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### [[:Category:High-Level Applications Symmetry|Symmetry]]
 
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### [[:Category:High-Level Applications Electron Density|Electron Density]]
 
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## [[:Category:High-Level Applications NMR Applications|NMR Applications]]
 
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### [[:Category:High-Level Applications Working with a Family of Structures|Working with Structure Families]]
 
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### [[:Category:High-Level Applications Superimposition and RMSD|Superimposition and RMSD]]
 
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### [[:Category:High-Level Applications NMR Restraints Analysis|NMR Restraints and Analysis]]
 
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# [[:Category:Third Party Software|Third Party Software]]
 
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## [[:Category:Third Party Software Movies|Movies]]
 
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## [[:Category:Third Party Software Codecs|Codecs]]
 
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# [[:Category:Python Integration|Python Integration]]
 
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# [[:Category:Using PyMol For Unintended Uses|Unintended Uses]] (OpenGL Object Renderer)
 
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## [[:Category:Using PyMol For Unintended Uses Arbitrary Graphics Objects| Arbitrary Graphics Objects]]
 
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# [[:Category:Uncategorized|Uncategorized]] For new pages, misplaced pages, etc.
 
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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...

Pse export version

The pse_export_version setting switches to a legacy format when saving PSEs, so far possible. The value is the floating point number representation of the targeted legacy PyMOL version, for example 1.74 to save a session for PyMOL 1.7.4.

New in PyMOL 1.7.6

Session file loading is always backwards compatible, so any newer version of PyMOL can load old session files.

Examples

# current version (default)
set pse_export_version, 0
save current.pse

# compatible with PyMOL 1.7.4
set pse_export_version, 1.74
save 174compat.pse

Known Limitations

The following objects are not or only partly supported:

  • scenes before 1.7.6 (support added in 1.8.4)
  • volumes before 1.7.2
  • ramps
  • CGOs

See Also
A Random PyMOL-generated Cover. See Covers.


Retrieved from "http://wiki.pymol.org/index.php?title=Main_Page&oldid=14896"