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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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| 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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| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
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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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! style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
 
 
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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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| 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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! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
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||'''[[PyMOL_mailing_list|Getting Help]]'''
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| [[TOPTOC|'''Table of Contents''']] -- ''updated!''
 
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|| [[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''']]
 
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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="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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! Official Release
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
 
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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;"| ♦ 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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! POSF
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
 
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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.
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! Tutorial
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| [[Plugins Tutorial]] updated for PyQt5
 
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| style="padding: 3px 5px 10px 15px;"| ♦ Information about PyMOL and [[Stereo_3D_Display_Options|Stereo 3D Displays]].
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! New Plugin
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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;"| ♦ Massively restructured the [[TOPTOC]] and make the [[OLD_TOPTOC]] for the older version. Still need to add more content to the [[TOPTOC]].
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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;"| ♦ Added a simple script for [[removeAlt|removing specific alternately located atoms]].
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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;"| ♦ Added a starter gallery of PyMOL-created Journal [[Covers]].
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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;"| ♦ Added some information on how PyMOL handles [[Nonstandard_Amino_Acids]].
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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;"| &diams; Downtime: The PyMOLWiki underwent some downtime due to FS problems.  There are also upgrades planned for this week, so we may expect a little downtime for that.  We've been <b>very</b> fortunate to have hosting from [http://www.bitgnome.net/ BitGnome.Net]; they've done an incredible job!
 
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| style="padding: 3px 5px 10px 15px;"| &diams; [[Gallery]] -- Did you make a [[:Image:Ccp4_map.png|cool image]]?  Pop it into the PyMOLWiki Gallery with the PyMOL command you used.  Looking for a particular representation--start here (new!).
 
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|valign="bottom" width="150px" style="padding: 0 20px 20px 0; clear:right;" |[[Image:070920nature.pdf.jpg|125px]] Sample Cover from the [[Covers]] gallery.
 
 
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| style="padding: 3px 5px 10px 15px;"| &diams; 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;"| &diams; [[group]] command has been added.
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| style="padding: 3px 5px 10px 15px;"| &diams; The truly awesome [[grid_mode]] setting has been added.
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| style="padding: 3px 5px 10px 15px;"| &diams; [[Ellipsoids]] representation added for drawing thermal ellipsoids.
 
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|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Gm1.png|125px]] Screenshot of [[grid_mode|Grid Mode]] in action.
 
 
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| style="padding: 3px 5px 10px 15px;"| &diams;  [[LigAlign]] -- Ligand-based active site alignment and comparison.
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listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
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| style="padding: 3px 5px 10px 15px;"| &diams; Added a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
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| style="padding: 3px 5px 10px 15px;"| &diams; [[ImmersiveViz]] -- Headtracking user interface for PyMOL (watch the video)!
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| style="padding: 3px 5px 10px 15px;"| &diams; [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars
 
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| style="padding: 3px 5px 10px 15px;"| &diams; [http://ase-web.rit.edu/~ez-viz/ProMOL_dl.html ProMOL] plugin added.  Catalytic site prediction, other tools.  Redirects to website.
 
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| style="padding: 3px 5px 10px 15px;"| &diams; [[EMovie]] plugin added. Easy movies in PyMol using a GUI.
 
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| style="padding: 3px 5px 10px 15px;"| &diams; [[DYNMAP]] plugin page created.  Check it out!
 
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| style="padding: 3px 5px 10px 15px;"| &diams; [[EZ-Viz]]
 
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|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:COLORAMA-screenshot.jpg|125px]] Screenshot of [[Colorama]].
 
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Latest revision as of 03:21, 22 June 2021

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 v2.5 has been released on May 10, 2021.
Python 3 New Python 3 compatibility guide for scripts and plugins
POSF New PyMOL fellows announced for 2018-2019
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 shadow mode

== Overview ==

Sets whether or not PyMol renders shadows casted onto labels and whether or not the labels themselves cast shadows.

Values

  • 0, no shadows
  • 1, object shadows are projected onto the labels, but the labels don't cast shadows
  • 2, object shadows are projected onto the labels, AND the lables DO cast shadows
  • 3, object shadows are NOT projected onto the labels, BUT the lables DO cast shadows.

Syntax

set label_shadow_mode, 0  # turn off shadows projected onto lables, turn off shadows cast from labels
set label_shadow_mode, 1  # turn on shadows projected onto labels, turn off shadows cast from labels
set label_shadow_mode, 2  # turn off shadows projected onto lables, turn on shadows cast from labels
set label_shadow_mode, 3  # turn on shadows projected onto lables, turn on shadows cast from labels
A Random PyMOL-generated Cover. See Covers.


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