Difference between revisions of "Main Page"

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|+ style="font-size:190%; font-weight: bold; color:#038; text-align:center; padding: 5px; margin-bottom: 15px" | Welcome to the PyMOL Wiki
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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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|- 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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|+ 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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! style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
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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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| 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]]!
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| To request a new account, email SBGrid at: accounts (@) sbgrid dot org
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! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
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| [[TOPTOC|'''Table of Contents''']] -- ''updated!''
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|-  
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|| [[Special:Allpages|Index of all pages]]
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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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|| '''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''']]
 
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|| [[: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;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
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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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||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
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==[http://www.surveymonkey.com/s.aspx?sm=NPHgdFVCWobsztKtjr5s5g_3d_3d Take the PyMOLWiki Survey! (click here)]==
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||'''[[PyMOL_mailing_list|Getting Help]]'''
 
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|+ 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]])
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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.
 
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| style="padding: 3px 5px 10px 15px;"| ♦ [[group]] command has been added.
 
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| style="padding: 3px 5px 10px 15px;"| ♦ The truly awesome [[grid_mode]] setting has been added.
 
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| style="padding: 3px 5px 10px 15px;"| ♦ [[Ellipsoids]] representation added for drawing thermal ellipsoids.
 
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|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Caver.png|125px]] Screenshot of [[Caver]] showing cavities.
 
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! Official Release
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| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
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! 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.
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! New Plugin
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| [[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;"| ♦ [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
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! Official Release
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
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| style="padding: 3px 5px 10px 15px;"| ♦ [[GetNamesInSel]] — find the names of all objects in a selection.
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! Python 3
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
 
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| style="padding: 3px 5px 10px 15px;"| ♦ [[CalcArea]] — find the area of any given object/selection;
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! POSF
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| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
 
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| style="padding: 3px 5px 10px 15px;"| ♦ [[ConnectedCloud]] — find connected clouds of objects in PyMOL.
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! Tutorial
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| [[Plugins Tutorial]] updated for PyQt5
 
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| 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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| [[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;"| ♦ [[DrawBoundingBox]] — Draw a bounding box around your selection.
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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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| style="padding: 3px 5px 10px 15px;"| ♦ Locate loaded PyMOL objects that are nearby some other object with [[FindObjectsNearby]].
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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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| 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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! 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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| style="padding: 3px 5px 10px 15px;"| ♦  [[PDB Web Services Script]] — Example using PyMOL and the PDB Web Services.
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! Older News
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| See [[Older_News|Older News]].
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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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|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="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;"| ♦ '''Please note the "Go" and "Search" buttons in the search bar. They're not the same, and entering text and hitting ENTER is the same as using the "Go" button.'''
 
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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;"| &diams; New category about PyMOL [[:Category:Performance|performance]]: making the impossible possible, and the difficult easier/faster.
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|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.
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Latest revision as of 12:54, 12 March 2024

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 v3.0 has been released on March 12, 2024.
New Plugin CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models
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 fellowship announced for 2022-2023
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...

Label size

== Overview ==

Sets how large the labels are rendered. You can use positive numbers 2, 3, 4, etc for point sizes, or negative numbers for Angstrom-based sizes. Default is 14 points. Labels in Angstrom-size scale with the distance from the front plane, labels in point-size don't. This automatic scaling works with the draw command but not with the ray command.

Syntax

# set the label size to 10pt
set label_size, 10

# set the label size to 1.5 Ang. -- large!
set label_size, -1.5
A Random PyMOL-generated Cover. See Covers.


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