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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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== [[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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* [[Mouse Controls]]
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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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* [[Command Language]]
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|-
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* [[Atom Selections]]
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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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* [[Ray-tracing]]
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|-
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* [[Movies and Animations]]
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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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* [[Cartoon Representations]]
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|-
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* [[Settings Reference (all settings and what they do)]]
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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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* [[Stereo 3D Display]]
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||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
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** [[Hardware Options]]
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||'''[[PyMOL_mailing_list|Getting Help]]'''
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** [[Linux XFree86 Configuration]]
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|}
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* [[Crystallography Aplications]]
 
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** [[Symmetry]]
 
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** [[Electron Density]]
 
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* [[Arbitrary Graphics Objects]]
 
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* [[Python Integration]]
 
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* [[Scenes]]
 
  
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== [[User Additions]] ==
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{| width="100%"
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* [[NMR Applicaitons]] (Doug Kojetin)
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| style="vertical-align: top; width: 40%" |
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* [[Plugins/Modules]] (Doug Kojetin)
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{| class="jtable" style="float: left; width: 90%;"
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** [[APBS Plugin]]
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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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* [[Plugins]] (Michael George Werner)
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! Official Release
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** [[List of Plugins]]
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
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** [[Tutorial on writing plugins]]
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|-
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** [[Others]]
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! Python 3
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
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* [[Structure Alignment]] (Nat Echols)
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|-
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** [[Structure Alignment Editor]]
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! POSF
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* [[3rd Party Applications]]
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
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** [[Movies]]
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|-
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** [[Codecs]]
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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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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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|
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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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02:06, 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...

Optimize

Type PyMOL Plugin
Download plugins/optimize.py
Author(s) Osvaldo Martin
License MIT
This code has been put under version control in the project Pymol-script-repo

Introduction

Optimize provides a PyMOL graphical interface to some of the molecular mechanics features available in openbabel, allowing the user to optimize (minimize) the energy of any molecule uploaded on PyMOL.

Installation

The plugin can be downloaded through the project Pymol-script-repo.

Optimize needs OpenBabel (and OpenBabel Python bindings) to be installed on your computer (see instructions here).

Note to Windows users: If you are using a 64-bit Windows, please install OpenBabel 64-bit from here

Usage

The plugin can be accessed using a graphic user interface (see figure 0) or from the PyMOL`s terminal. There are 5 types of optimization routines available now, 2 local and 3 global optimization routines.

== Local ..→

A Random PyMOL-generated Cover. See Covers.


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