Difference between revisions of "Main Page"

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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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|
 
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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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| For Educational downloads go to http://pymol.org/educational
 
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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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| 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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| 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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| 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 Script
 
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| [[ColorByDisplacement]] Do an (specified) alignment of residues between an open and closed form of a protein. Calculates the distance displacement between each residue and saves it as its b-factor. Then it color according to the b-factor. Quite neat feature for rotation axis in proteins.
 
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|-
 
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! New Script
 
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| [[DisplacementMap]] Calculates CA-CA distances between Open and Closed form of protein. Output best suggestions for site-directed mutagenesis for EPR/FRET experiments. Make distance matrix file, and output a gnuplot plot file for easy visualisation of interesting residues. Parses best suggestions back to pymol, for visual inspections.
 
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! New Script
 
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| Two new scripts: [[AAindex]] and [[Sidechaincenters]]
 
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|-
 
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! New Plugin
 
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| [[CAVER_2.0]] update to the CAVER plugin.
 
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|-
 
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! New Script
 
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| [[AngleBetweenHelices]] calculates the angle between two helices.
 
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|-
 
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! Search
 
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| [[GoogleSearch]] widget fixed.
 
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|-
 
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! New Script
 
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| [[Spectrumany]] creates color gradients with arbitrary color sequences.
 
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! New Script
 
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| [[BbPlane]] will draw CGO planes across the backbone highlighting planarity of arrangement.
 
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! New Script
 
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| [[Center Of Mass]] has been re-written to calculate either the center-of-geometry or (mass-weighted) center-of-mass for a given selection and represents that selection as a pseudoatom (rather than a CGO sphere). 
 
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|-
 
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! New Script
 
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| [[Jump]] is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL.
 
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|-
 
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! New Scripts
 
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| [[ResDe]] is a suite of programs designed to assist crystallographers in defining user defined hydrogen bond distance restraints, which can be helpful when refining low-resolution structures.
 
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|-
 
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! New Script
 
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| See [[BiologicalUnit]], for a workaround to the buggy [[Symexp]] command or if you just want to learn more about symmetry expansion in PyMOL.
 
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|-
 
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! New Script
 
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| See [[Supercell]], the new script for making XxYxZ supercells.
 
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! New Script
 
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| See [[Split_Object_Along_Axis]], for a script that allows one to select a bond, and then generate 2 selections: one for the selection of all atoms that are on one side of this bond, and the other selection for the atoms on the other side of the bond.
 
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! New Script
 
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| See [[Consistent_View/_Map_Inspect]], which is a toolkit for rapidly inspecting multiple maps and models.
 
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! Server updates
 
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| The underlying servers upon which the PyMOLWiki runs were upgraded over the weekend.  We are now fully functional.  A '''deep''' thanks to [http://www.bitgnome.net BitGnome] for donating time and hardware for the PyMOL project.
 
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! fetch_host setting
 
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| [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice.
 
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! Fetch
 
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| [[Fetch]] has been updated to also load electron density maps.
 
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|-
 
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! Schrodinger Buys PyMOL
 
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| Schrodinger has purchased PyMOL.  Development, support and open-source fun to continue!  Read about the [http://www.schrodinger.com/news/47/ sale].
 
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! User Movie
 
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| One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL. 
 
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|-
 
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! New setting
 
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| [[surface_cavity_mode]] to change how PyMOL displays cavities.
 
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|-
 
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! Search fixed.
 
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| Thanks to a eagle-eyed user, our search has been fixed.  Please let us know if you have any search-related problems.
 
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|-
 
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! New Command
 
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| [[Cache]]—stores information on structures, so we don't have to recompute them.
 
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! Warren
 
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| News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]].
 
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|-
 
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! Setting
 
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| [[Fetch_Path]]—Sets the default path for the [[fetch]] command.
 
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|-
 
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! New Script
 
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| [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box.
 
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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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|<div class="didyouknow" >
 
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