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| __NOTOC__ | | __NOTOC__ |
− | {| align="center" width="90%" | + | {| 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;" |
− | |+ style="font-size:190%; font-weight: bold; color:#038; text-align:center; padding: 5px; margin-bottom: 15px" | Welcome to the PyMOL Wiki | + | |+ 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/]] |
− | |- style="text-align:center; font-weight:bold; color: #333; font-size: 120%"
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− | | We are the community-based support site for the popular molecular visualization program, [http://pymol.sf.net PyMOL]. | |
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| |} | | |} |
− | {| align="center" style="width:90%; margin-bottom: 20px" | + | {| align="center" style="padding-bottom: 3em;" |
− | | | + | |+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki! |
− | {| align="left" width="20%" style="border: 1px solid #333; text-align:center; height=100%;"
| + | |- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;" |
− | ! style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
| + | | The community-run support site for the [http://pymol.org PyMOL] molecular viewer. |
− | |- | + | |- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;" |
− | | style="background:#E6EFFF; color:#333; font-size: 110%; padding: 4.5px"| New users are encouraged to [[Special:Userlogin|join]]. Feel free to add any appropriate content; make an account and [[PyMolWiki:Community_Portal|get started]]! | + | | 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;" |
| |} | | |} |
− | {| align="right" width="75%" style="border: 1px solid #333; text-align:left;" | + | |
− | ! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
| + | {| 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;" |
| + | |+ 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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| + | | 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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− | | [[TOPTOC|'''Table of Contents''']] -- ''updated!'' | + | | 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]]''' |
− | || [[Special:Allpages|Index of all pages]]
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− | || '''PyMOL Cheat Sheet: [[Media:PymolRef.pdf|PDF]] | [[CheatSheet|Wiki Page]]
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− | | [[:Category:Tutorials|Tutorials]]
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− | || [[:Category:Commands|Commands]]
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− | || '''Settings''': [[Settings|All]] | [[:Category:Settings|Documented]]
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− | | [[:Category:Script_Library|'''Script Library''']]
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− | || [[:Category:Plugins|'''Plugins''']] | |
− | || [[:Special:Categories| See All Categories]]
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− | | [[:Category:FAQ|Frequently Asked Questions]]
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− | || [[Gallery|'''Gallery''']] | [[Covers|'''Covers''']]
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− | || [[About| '''About PyMOL''']]
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− | | ''Track:'' [http://sourceforge.net/tracker/?atid=104546&group_id=4546&func=browse Bugs] [http://sourceforge.net/tracker/?group_id=4546&atid=354546 Feature Req] [http://sourceforge.net/tracker/?group_id=4546&atid=204546 Support Req]
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| + | | style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]''' |
| + | ||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'') |
| + | ||'''[[PyMOL_mailing_list|Getting Help]]''' |
| |} | | |} |
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− | |}
| + | {| width="100%" |
− | {| align="center" width="90%" style="background: #fafafa; border-right: 1px solid #333; border-left: 1px solid #333; border-bottom: 1px solid #333" | + | | style="vertical-align: top; width: 40%" | |
− | |+ style="text-align: left; font-weight:bold; font-size:150%; color:#333; background: #EFE6FF; padding:10px; border: 1px solid #333" | News and Updates ([[Older_News|archive]]) | + | {| 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 |
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− | ! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
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− | | style="padding: 3px 5px 10px 15px;"| ♦ '''PyMOL now integrates seamlessly with MS Powerpoint. See [[Axpymol]].'''
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− | | style="padding: 3px 5px 10px 15px;"| ♦ PyMOL now comes with some builtin examples: look in the '''examples''' directory of your source tree. | + | ! Official Release |
| + | | [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024. |
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− | | style="padding: 3px 5px 10px 15px;"| ♦ [[group]] command has been added. | + | ! New Plugin |
| + | | [[CavitOmiX|CavitOmiX]] calculate [https://innophore.com Catalophore™ cavities], predict protein structures with [https://www.nvidia.com/en-us/gpu-cloud/bionemo OpenFold by NVIDIA-BioNeMo], [https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/ ESMFold] and retrieve [https://www.deepmind.com/research/highlighted-research/alphafold Alphafold] models |
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− | | style="padding: 3px 5px 10px 15px;"| ♦ The truly awesome [[grid_mode]] setting has been added. | + | ! Official Release |
| + | | [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021. |
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− | | style="padding: 3px 5px 10px 15px;"| ♦ [[Ellipsoids]] representation added for drawing thermal ellipsoids.
| + | ! Python 3 |
− | |}
| + | | New [[2to3|Python 3 compatibility guide]] for scripts and plugins |
− | |valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Caver.png|125px]] Screenshot of [[Caver]] showing cavities. | |
− | |}
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| + | ! POSF |
− | {|style="background-color: transparent;" width="100%"
| + | | [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023] |
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| + | ! Tutorial |
− | {|style="background-color: transparent;" width="100%"
| + | | [[Plugins Tutorial]] updated for PyQt5 |
− | ! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts & Plugins
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− | | style="padding: 3px 5px 10px 15px;"| ♦ [[Modevectors]] — creates arrow plots for normal mode analysis (NMA), NMR ensembles and other cases where you want to point out differences between similar objects. | + | ! New Plugin |
| + | | [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe |
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− | | style="padding: 3px 5px 10px 15px;"| ♦ [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection. | + | ! Selection keywords |
| + | | 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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− | | style="padding: 3px 5px 10px 15px;"| ♦ [[GetNamesInSel]] — find the names of all objects in a selection. | + | ! Plugin Update |
| + | | [[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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− | | style="padding: 3px 5px 10px 15px;"| ♦ [[CalcArea]] — find the area of any given object/selection; | + | ! New Script |
| + | | [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons |
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− | | style="padding: 3px 5px 10px 15px;"| ♦ [[ConnectedCloud]] — find connected clouds of objects in PyMOL.
| + | ! Older News |
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| + | | See [[Older_News|Older News]]. |
− | | style="padding: 3px 5px 10px 15px;"| ♦ [[MakeVinaCommand]] — Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.
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− | | style="padding: 3px 5px 10px 15px;"| ♦ [[DrawBoundingBox]] — Draw a bounding box around your selection.
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− | | style="padding: 3px 5px 10px 15px;"| ♦ Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
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− | | style="padding: 3px 5px 10px 15px;"| ♦ Ever wanted to load all the PDBs in a directory within PyMOL? Now you can load all files in a dir with [[LoadDir]].
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− | | style="padding: 3px 5px 10px 15px;"| ♦ [[PDB Web Services Script]] — Example using PyMOL and the PDB Web Services.
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− | | style="padding: 3px 5px 10px 15px;"| ♦ [[LigAlign]] — Ligand-based active site alignment and comparison.
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− | | style="padding: 3px 5px 10px 15px;"| ♦ Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
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− | |}
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− | |width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:DrawMinBB.png|165px]] Screenshot of [[DrawBoundingBox]] in action.
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| |} | | |} |
− | {|style="background-color: transparent;" width="100%"
| + | |style="vertical-align: top; width: 40%"| |
− | |- | + | {| class="jtable" style="float: right; width: 90%" |
− | |valign="top"| | + | |+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know... |
− | {|style="background-color: transparent;" width="100%"
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− | ! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
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− | | style="padding: 3px 5px 10px 15px;"| ♦ Documented a few more settings. Also, check out the cool, [[Huge_surfaces]] page for handling very large objects and representing them as surfaces, in PyMOL.
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− | | style="padding: 3px 5px 10px 15px;"| ♦ We got our '''2,000,000th''' page view!
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− | | style="padding: 3px 5px 10px 15px;"| ♦ Added links in the table on the Main Page (above) for submitting & tracking bugs and feature reqeuests.
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− | | style="padding: 3px 5px 10px 15px;"| ♦ New logo for the wiki. It's DNA. You can easily see the major/minor grooves. If you don't see it, force a reload of the page (CTRL-F5, usually).
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− | | style="padding: 3px 5px 10px 15px;"| ♦ New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster. | + | |<div class="didyouknow" > |
− | |}
| + | <DynamicPageList> |
− | |valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:080701_h.a.steinberg_biochemie.jpg|125px]] Sample Cover from the [[Covers]] gallery.
| + | randomcount=1 |
| + | category=Commands|Plugins|Script_Library|Settings |
| + | includepage=* |
| + | includemaxlength=1050 |
| + | escapelinks=false |
| + | allowcachedresults=false |
| + | resultsheader=__NOTOC__ __NOEDITSECTION__ |
| + | listseparators=,<h3>[[%PAGE%]]</h3>,,\n |
| + | </DynamicPageList> |
| + | </div> |
| + | <div style="clear: both;"></div> |
| |} | | |} |
| + | | |
| + | |style="vertical-align: top; width: 18%"| |
| + | <DynamicPageList> |
| + | imagecontainer=Covers |
| + | randomcount=1 |
| + | escapelinks=false |
| + | openreferences=true |
| + | listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover. See [[Covers]].]],\n |
| + | ordermethod=none |
| + | allowcachedresults=false |
| + | </DynamicPageList> |
| + | |
| |} | | |} |