Difference between revisions of "Main Page"

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|+ style="width: 90%; 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 join. Feel free to add any appropriate content; make an account and 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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||'''[[PyMOL_mailing_list|Getting Help]]'''
 
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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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|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
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| [[TOPTOC|'''Table of Contents''']]
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! Official Release
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|| [[Special:Allpages|Index of all pages]]
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| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
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|| [http://pymol.sf.net PyMOL] Homepage
 
 
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| [[Practical_Pymol_for_Beginners|Beginner's Tutorial]]
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! New Plugin
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|| [[:Category:Commands|PyMol Commands]]
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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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|| '''Settings''': [[Settings|All]] [[:Category:Settings|Documentented]]
 
 
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| [[:Category:Script_Library|'''Script Library''']]
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! Official Release
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|| [[:Category:Plugins|'''Plugins''']]
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| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
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|| [[:Special:Categories| See All Categories]]
 
 
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| [[:Category:FAQ|Frequently Asked Questions]]
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! Python 3
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|| [[PyMolWiki:Community_Portal|'''How to get involved!''']]
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| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
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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="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="padding: 3px 5px 10px 15px;"| ♦ Rather large changes to the style of the main page.  Hopefully this will transition into something more pleasing.
 
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| style="padding: 3px 5px 10px 15px;"| ♦ We need experienced PyMOL users to link pages to their respective categories and make new categories.  Some new categories that need to be filled: [[:Category:Settings]], [[:Category:Publication_Quality]], [[:Category:Image_Manipulation]], [[:Category:Nucleic_Acids]]. We also need a category -- or categories -- on biochemical analysis and other useful things we do in PyMOL.  This will help people expand their knowledge (by being able to see related issues), and make it easier for the power users to find what they need.  The editing is '''very simple''' -- all you do is add a category tag(s) at the end of the pages.
 
 
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| style="padding: 3px 5px 10px 15px;"| ♦  We also need folks to link to the pages in the [[Special:Lonelypages|Orphaned Pages]].  These pages are only found by direct searching, so we should change that to help make this more usable.
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! Tutorial
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| [[Plugins Tutorial]] updated for PyQt5
 
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px" | PyMOL
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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;"| ♦ PyMOL 1.0 has been released!
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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;"| ♦ [http://delsci.info/dsc/ PyMOL Official Documentation] is also available for subscribers.
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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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! 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;"| ♦ [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars
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! Older News
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| See [[Older_News|Older News]].
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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="padding: 3px 5px 10px 15px;"| ♦ [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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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...

Align

Two proteins after structure alignment

align performs a sequence alignment followed by a structural superposition, and then carries out zero or more cycles of refinement in order to reject structural outliers found during the fit. align does a good job on proteins with decent sequence similarity (identity >30%). For comparing proteins with lower sequence identity, the super and cealign commands perform better.

Usage

align mobile, target [, cutoff [, cycles
    [, gap [, extend [, max_gap [, object
    [, matrix [, mobile_state [, target_state
    [, quiet [, max_skip [, transform [, reset ]]]]]]]]]]]]]

Arguments

  • mobile = string: atom selection of mobile object
  • target = string: atom selection of target object
  • cutoff = float: outlier rejection cutoff in RMS {default: 2.0}
  • cycles = int: maximum number of outlier rejection cycles {default: 5}
  • gap, extend, max_gap: sequence alignment parameters
  • object = ..→
A Random PyMOL-generated Cover. See Covers.


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