This is a read-only mirror of pymolwiki.org
Difference between revisions of "Main Page"
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− | . | + | __NOTOC__ |
+ | {| align="center" style="padding-bottom: 4em;" | ||
+ | |+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki! | ||
+ | |- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;" | ||
+ | | The community-run support site for the [http://pymol.org PyMOL] molecular viewer. | ||
+ | | | ||
+ | |- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-style: italic; font-family: serif;" | ||
+ | | | ||
+ | |- style="text-align:center; font-weight:bold; color: #6d6003; font-size: 140%; font-family: serif; font-style: italic;" | ||
+ | | For Educational downloads go to http://pymol.org/educational | ||
+ | | | ||
+ | |- style="text-align:center; font-weight:bold; color: #333; font-size: 140%; font-family: serif;" | ||
+ | | Due to large amounts of spam, we've halted unsupervised account creation. Please contact jason . vertrees (@) gmail dot com to get a new account. | ||
+ | |} | ||
+ | {| 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;" | ||
+ | |+ 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 | ||
+ | |- | ||
+ | | style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]''' | ||
+ | |- | ||
+ | | 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]]''' | ||
+ | |- | ||
+ | | style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]''' | ||
+ | ||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'') | ||
+ | ||'''[[GoogleSearch]]''' | ||
+ | |} | ||
− | . | + | {| width="100%" |
+ | | style="vertical-align: top; width: 40%" | | ||
+ | {| class="jtable" style="float: left; width: 90%;" | ||
+ | |+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates | ||
+ | |- | ||
+ | ! New Script | ||
+ | | There is a new script to calculate the [[Radius of gyration]] | ||
+ | |- | ||
+ | ! New Command | ||
+ | | [[Map_set]] Performs a given operation on a map: can create consensus volumes, for example. | ||
+ | |- | ||
+ | ! New Script | ||
+ | | [[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. | ||
+ | |- | ||
+ | ! New Script | ||
+ | | [[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. | ||
+ | |- | ||
+ | ! New Script | ||
+ | | Two new scripts: [[AAindex]] and [[Sidechaincenters]] | ||
+ | |- | ||
+ | ! New Plugin | ||
+ | | [[CAVER_2.0]] update to the CAVER plugin. | ||
+ | |- | ||
+ | ! New Script | ||
+ | | [[AngleBetweenHelices]] calculates the angle between two helices. | ||
+ | |- | ||
+ | ! Search | ||
+ | | [[GoogleSearch]] widget fixed. | ||
+ | |- | ||
+ | ! New Script | ||
+ | | [[Spectrumany]] creates color gradients with arbitrary color sequences. | ||
+ | |- | ||
+ | ! New Script | ||
+ | | [[BbPlane]] will draw CGO planes across the backbone highlighting planarity of arrangement. | ||
+ | |- | ||
+ | ! New Script | ||
+ | | [[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). | ||
+ | |- | ||
+ | ! New Script | ||
+ | | [[Jump]] is a tool for jumping from one frame to another when you have a movie, MD simulation, or multiple models loaded into PyMOL. | ||
+ | |- | ||
+ | ! New Scripts | ||
+ | | [[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. | ||
+ | |- | ||
+ | ! New Script | ||
+ | | See [[BiologicalUnit]], for a workaround to the buggy [[Symexp]] command or if you just want to learn more about symmetry expansion in PyMOL. | ||
+ | |- | ||
+ | ! New Script | ||
+ | | See [[Supercell]], the new script for making XxYxZ supercells. | ||
+ | |- | ||
+ | ! New Script | ||
+ | | 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. | ||
+ | |- | ||
+ | ! New Script | ||
+ | | See [[Consistent_View/_Map_Inspect]], which is a toolkit for rapidly inspecting multiple maps and models. | ||
+ | |- | ||
+ | ! Server updates | ||
+ | | 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. | ||
+ | |- | ||
+ | ! fetch_host setting | ||
+ | | [[Fetch_Host]] has been added to allow users to download PDBs from their PDB server (pdb, pdb euro, or pdb japan) of choice. | ||
+ | |- | ||
+ | ! Fetch | ||
+ | | [[Fetch]] has been updated to also load electron density maps. | ||
+ | |- | ||
+ | ! Schrodinger Buys PyMOL | ||
+ | | Schrodinger has purchased PyMOL. Development, support and open-source fun to continue! Read about the [http://www.schrodinger.com/news/47/ sale]. | ||
+ | |- | ||
+ | ! User Movie | ||
+ | | One of our users has posted another [http://www.youtube.com/watch?v=eQWw6x3fLF0 interesting movie], images from which were created with PyMOL. | ||
+ | |- | ||
+ | ! New setting | ||
+ | | [[surface_cavity_mode]] to change how PyMOL displays cavities. | ||
+ | |- | ||
+ | ! Search fixed. | ||
+ | | Thanks to a eagle-eyed user, our search has been fixed. Please let us know if you have any search-related problems. | ||
+ | |- | ||
+ | ! New Command | ||
+ | | [[Cache]]—stores information on structures, so we don't have to recompute them. | ||
+ | |- | ||
+ | ! Warren | ||
+ | | News about Warren DeLano's passing may be read on [[Warren|Warren's memorial page]]. | ||
+ | |- | ||
+ | ! Setting | ||
+ | | [[Fetch_Path]]—Sets the default path for the [[fetch]] command. | ||
+ | |- | ||
+ | ! New Script | ||
+ | | [[SelInside]]—Creates a custom selection of all atoms spatially inside some user-defined box. | ||
+ | |} | ||
+ | |style="vertical-align: top; width: 40%"| | ||
+ | {| class="jtable" style="float: right; width: 90%" | ||
+ | |+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know... | ||
+ | |- | ||
+ | |<div class="didyouknow" > | ||
+ | <DPL> | ||
+ | namespace= | ||
+ | category=Commands|Plugins|Script_Library|Settings | ||
+ | includepage=* | ||
+ | includemaxlength=450 | ||
+ | escapelinks=false | ||
+ | resultsheader=__NOTOC__ __NOEDITSECTION__ | ||
+ | randomcount=1 | ||
+ | mode=userformat | ||
+ | addpagecounter=true | ||
+ | listseparators=,<h3>[[%PAGE%]]</h3>,,\n | ||
+ | </DPL> | ||
+ | </div> | ||
+ | <div style="clear: both;"></div> | ||
+ | |} | ||
+ | | | ||
+ | |style="vertical-align: top; width: 18%"| | ||
+ | <DPL> | ||
+ | imagecontainer=Covers | ||
+ | randomcount=1 | ||
+ | escapelinks=false | ||
+ | openreferences=true | ||
+ | listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n | ||
+ | ordermethod=none | ||
+ | </DPL> | ||
− | + | |} | |
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Revision as of 19:04, 31 March 2011
The community-run support site for the PyMOL molecular viewer. | |
For Educational downloads go to http://pymol.org/educational | |
Due to large amounts of spam, we've halted unsupervised account creation. Please contact jason . vertrees (@) gmail dot com to get a new account. |
Tutorials | Table of Contents | Commands |
Script Library | Plugins | FAQ |
Gallery | Covers | PyMOL Cheat Sheet (PDF) | GoogleSearch |
|
|
![]() A Random PyMOL-generated Cover. See Covers.
|