Difference between revisions of "Main Page"

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* [[Special:Allpages|Alphabetized Index of all pages]]
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{| align="center" style="padding-bottom: 3em;"
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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:center; font-weight:bold; color: #000000; font-size: 120%; font-family: sans-serif;"
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|}
  
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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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|-
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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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||'''[[PyMOL_mailing_list|Getting Help]]'''
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|}
  
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== Welcome to the PyMOL Wiki ==
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You have reached the home of the PyMolWiki, a user-driven web-oriented CMS.
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| style="vertical-align: top; width: 40%" |
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{| class="jtable" style="float: left; width: 90%;"
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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News &amp; Updates
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|-
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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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|-
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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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|-
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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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|-
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! Python 3
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
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|-
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! POSF
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| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
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|-
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! Tutorial
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| [[Plugins Tutorial]] updated for PyQt5
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|-
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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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|-
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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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|-
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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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|-
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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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|-
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! Older News
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| See [[Older_News|Older News]].
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|}
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{| class="jtable" style="float: right; width: 90%"
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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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We provide
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* Updates on [http://pymol.sf.net PyMol]
 
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* User-maintained documentation
 
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** [[Practical_Pymol_for_Beginners|Beginner's Tutorial]]
 
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* PyMOL Scripts
 
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** [[:Category:Script_Library|feature-rich scripts]] for general PyMol use
 
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== New Users ==
 
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Welcome!  New users who wish to contribute appropriate content are welcome to join.  Feel free to add any appropriate content; make an account and get started!
 
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==News ([[Older_News|archive]])==
 
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===Wiki===
 
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* Many search terms were missing due to normal pages acting as category pages.  Now searches for '''mencoder''', and '''publication quality images''' should now result in non-empty matches.  This should make finding things on the PyMOLWiki much easier.
 
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* '''The PyMolWiki has now had over 1,000,000 impressions!'''  The community accesses the resources on the wiki at rate of '''over 1,000 hits a day''' and is steadily growing.  See the [[Special:Statistics|Statistics]].
 
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===PyMol===
 
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* Pymol 1.0 is out!
 
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* [http://delsci.info/dsc/ PyMol Official Documentation] is also available for subscribers.
 
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===Plugins/Scripts===
 
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* [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars
 
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* [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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* [[EMovie]] plugin added.  Easy movies in PyMol using a GUI.
 
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* [[DYNMAP]] plugin page created.  Check it out!
 
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== Links of Interest ==
 
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* [[TOPTOC|Top Level Table of Contents]]
 
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* [[:Category:FAQ|Frequently Asked Questions]]
 
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* [[PyMolWiki:Community_Portal| How to get involved!]]
 
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* [[:Category:Script Library| Script Library]]
 
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* [[:Category:Commands|PyMol Commands]]
 
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* [[Settings|PyMol Settings]]
 
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* [[:Special:Allpages| All Pages]]
 
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* [[:Category:Plugins|Plugins]]
 
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* [[:Special:Categories| See All Categories]]
 

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...

Ray trace disco factor

The ray_trace_disco_factor setting has an effect on ray_trace_mode 1-3. With small values, outlines will appear at surface curvature discontinuities.
set ray_trace_disco_factor, 0.0 set ray_trace_disco_factor, 1.0
Ray trace disco factor-0-cartoon.png Ray trace disco factor-1-cartoon.png
Ray trace disco factor-0-spheres.png Ray trace disco factor-1-spheres.png
Ray trace disco factor-0-sticks.png Ray trace disco factor-1-sticks.png

Usage

set ray_trace_mode
set ray_trace_disco_factor, 1.0 ;# disable effect
set ray_trace_disco_factor, 0.1 ;# some outlines
set ray_trace_disco_factor, 0.0 ;# strong outlines

Example

# load a molecule
fragment indane
show_as spheres

# white background makes black outlines
bg_color white

# enable outline mode
set ray_trace_mode, 3
set ray_trace_disco_factor, 0.0
ray

See Also
A Random PyMOL-generated Cover. See Covers.


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