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'''MediaWiki has been successfully installed.'''
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{| align="center" style="padding-bottom: 4em;"
 
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|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
 
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|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: 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:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
 
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| New accounts: email jason (dot) vertrees (@) gmail dot com
 
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|- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;"
 
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|}
 
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{| align="center" width="45%" style="background: #EDEBD5; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
 
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|+ style="font-size: 1.4em; font-weight: bold; color: #032d45; text-align:center; background: #5F7F96; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #AFB29E; border-bottom: 1px solid #fff;" |Quick Links
 
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|-
 
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| style="font-size: 1.1em; color #61021F; 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; color #61021F; 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; color #61021F; 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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||'''[[GoogleSearch]]'''
 
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Consult the [//meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
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| style="vertical-align: top; width: 40%" |
 
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{| class="jtable" style="float: left; width: 90%;"
 
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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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! New Plugin
 
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
 
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|-
 
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! 3D using Geforce
 
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| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
 
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|-
 
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! New Plugin
 
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| [[Bondpack]] is a a collection of PyMOL plugins for easy visualization of atomic bonds.
 
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|-
 
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! New Plugin
 
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| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
 
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|-
 
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! New Software
 
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| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
 
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|-
 
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! New Script
 
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| [[cgo_arrow]] draws an arrow between two picked atoms.
 
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|-
 
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! Tips & Tricks
 
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| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
 
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|-
 
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! New Script
 
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| [[Cluster_Count|Cluster Count]] calculates statistics on the B-values for all atoms in the selected object.
 
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|-
 
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! New Script
 
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| [[Make_Figures|Make Figures]] aids you in making publication quality figures for the currently displayed scene.
 
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|-
 
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! New Script
 
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| [[DistancesRH|Distances RH]]
 
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|-
 
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! PyMOL on the iPad
 
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| PyMOL is now available on the iPad as a free download from the AppStore. See [http://pymol.org/mobile pymol.org/mobile] for more info.
 
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|-
 
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! OS X Compatibility
 
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| Mac OS X 10.8 doesn't ship with X11. But, you can get the libraries here [http://xquartz.macosforge.org/landing/ X11 Libraries].
 
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|-
 
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! New Script
 
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| [[select_sites]] can set author/paper selections according to SITE annotation in pdb file
 
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|-
 
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! New Script
 
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| [[b2transparency]] can set surface transparency based on atom b-factor
 
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|-
 
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! New Extension
 
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| [[psico]] is a python module which extends PyMOL with many commands
 
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|-
 
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! New Script
 
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| [[uniprot_features]] makes named selections for sequence annotations from uniprot
 
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|-
 
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! New Plugin
 
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| [[Gyration_tensor]] Calculates chain-wise gyration tensor of a protein.
 
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|-
 
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! New Script
 
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| [[set_phipsi]] can set phi/psi angles for all residues in a selection
 
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|-
 
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! New Script
 
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| [[dehydron]] A plugin to calculate dehydrons and display them onto the protein structure. A dehydron is a main chain hydrogen bond incompletely shielded from water attack.
 
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|-
 
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! New Script
 
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| [[pymol2glmol]] is script to export a scene in pymol to a webpage for GLmol. GLmol is a molecular viewer for Web browsers written in WebGL/Javascript. Like web Jmol, but MUCH faster. Try it out!
 
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|-
 
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! New Script
 
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| [[cyspka]] is an experimental surface cysteine pKa predictor.
 
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|-
 
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! New Plugin
 
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| [[Contact_Map_Visualizer]] visualize residues corresponding to the contact map. See [[CMPyMOL]].
 
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|-
 
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! New Script
 
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| [[spectrum_states]] colors states of multi-state object
 
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|-
 
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! New Script
 
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| [[TMalign]] is a wrapper for the TMalign program
 
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|-
 
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! Gallery Updates
 
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| The [[Gallery|gallery]] has been updated to include a few new ideas and scripts for rendering
 
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|-
 
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! New Script
 
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| [[save_settings]] can dump all changed settings to a file
 
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|-
 
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! Tips & Tricks
 
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| Instructions for [[3d_pdf|generating 3D PDFs]] using PyMOL.
 
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|-
 
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! Wiki Update
 
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| Wiki has been updated. Please report any problems to the sysops.
 
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|-
 
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! New Scripts
 
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| Create objects for each molecule or chain in selection with [[split_object]] and [[split_chains]]
 
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|-
 
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! New Script
 
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| [[Rotkit]]: is a collection of usefull scripts to place your dye/molecule where you want. It includes a very handy, rotation around line, function. 
 
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|-
 
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! New Script
 
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| [[Forster-distance-calculator]]: Can be used as a pymol-python shortcut to calculate the Förster distance between dyes from different companies. Useful, if the user have pymol installed, but not python. This script is meant as a tool to finding the right dyes, when labelling suitable positions for the site-directed cysteine mutants. See [[DisplacementMap]].
 
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|-
 
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! New Script
 
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| [[propka]]: Fetches the pka values for your protein from the [http://propka.ki.ku.dk/ propka] server. [[propka]] generates a pymol command file that make pka atoms, color and label them according to your protein. Inspection is made easy by grouping the pka atoms in the pymol menu.
 
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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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<DPL>
 
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<DPL>
 
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imagecontainer=Covers
 
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randomcount=1
 
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== Getting started ==
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* [//www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list]
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* [//www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
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* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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* [//www.mediawiki.org/wiki/Localisation#Translation_resources Localise MediaWiki for your language]

Revision as of 00:29, 28 March 2014

MediaWiki has been successfully installed.

Consult the User's Guide for information on using the wiki software.

Getting started

Retrieved from "http://wiki.pymol.org/index.php?title=Main_Page&oldid=1"