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-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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! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
 
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|-
 
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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="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="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-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: 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="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="padding: 3px 5px 10px 15px;"| ♦ [[Ellipsoids]] representation added for drawing thermal ellipsoids.
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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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|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Caver.png|125px]] Screenshot of [[Caver]] showing cavities.
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||'''[[PyMOL_mailing_list|Getting Help]]'''
 
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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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! 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;"| ♦ [[Pucker]] — finds the sugar pucker information (phase, amplitude, pucker) for a given selection.
 
 
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| style="padding: 3px 5px 10px 15px;"| ♦ [[GetNamesInSel]] — find the names of all objects in a selection.
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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;"| ♦ [[CalcArea]] — find the area of any given object/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;"| ♦ [[ConnectedCloud]] — find connected clouds of objects in PyMOL.
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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;"| ♦ [[MakeVinaCommand]] — Use PyMOL to create a valid command line for the new [http://vina.scripps.edu Vina] docking software.
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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;"| ♦ [[DrawBoundingBox]] — Draw a bounding box around your selection.
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! Tutorial
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| [[Plugins Tutorial]] updated for PyQt5
 
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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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! 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;"| ♦ 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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! 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;"| ♦  [[PDB Web Services Script]] — Example using PyMOL and the PDB Web Services.
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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;"| ♦  [[LigAlign]] — Ligand-based active site alignment and comparison.
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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 a [[COM|simple script]] for finding the center or mass, or moving a selection to the origin.
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! Older News
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| See [[Older_News|Older News]].
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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-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
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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.
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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...

Specular intensity

= Overview =

This controls how PyMOL displays specular reflections in the GUI (unrendered). This is analogous to Spec_power for ray traced images.

Values range form [0, 200+].

Syntax

# set the specular intensity to some real valued number
set specular_intensity, float

# for example, set it to 200
set specular_intensity, 200.0

See Also

Spec_power

A Random PyMOL-generated Cover. See Covers.


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