Difference between revisions of "Main Page"

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|+ style="font-size:210%; font-weight: bold; color:#032d45; text-align:center; padding: 5px; margin-bottom: 4px;" | 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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{| 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!
 +
|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
 
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
 
| 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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| New accounts: email jason (dot) vertrees (@) gmail dot com
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| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
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|-  
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| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
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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-size: 1.1em; color #61021F; 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;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
 
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| style="font-size: 1.1em; color #61021F; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
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| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
 
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
 
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
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||'''[[PyMOL_mailing_list|Getting Help]]'''
 
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{| class="jtable" style="float: left; width: 90%;"
 
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
 
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & 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.
 
|-
 
|-
 
! New Plugin
 
! New Plugin
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| [[Bondpack]] is a a collection of PyMOL plugins for easy visualization of atomic bonds.
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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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! New Plugin
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! POSF
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| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.0]] is a new plugin for rapid analysis of biomacromolecular channels in PyMOL.
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| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
 
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|-
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! 3D using Geforce
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! Tutorial
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| PyMOL can now be [http://forums.geforce.com/default/topic/571604/3d-vision/3d-vision-working-with-qbs-in-opengl-software-using-geforce/2/ visualized in 3D using Nvidia GeForce video cards] (series 400+) with 120Hz monitors and Nvidia 3D Vision, this was previously only possible with Quadro video cards.
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| [[Plugins Tutorial]] updated for PyQt5
 
|-
 
|-
 
! New Plugin
 
! New Plugin
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| [[GROMACS_Plugin]] is a new plugin that ties together PyMOL and GROMACS.
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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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! New Software
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! Selection keywords
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| [[CMPyMOL]] is a software that interactively visualizes 2D contact maps of proteins in PyMOL.
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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]!
 +
|-
 +
! Plugin Update
 +
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
 
|-
 
|-
 
! New Script
 
! New Script
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| [[cgo_arrow]] draws an arrow between two picked atoms.
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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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! Tips & Tricks
 
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| Instructions for [[Movie_pdf|generating movie PDFs]] using .mpg movies from PyMOL.
 
 
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! Older News
 
! Older News
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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...

AutoMultiFit

= OVERVIEW =

AutoMultiFit will fit all given chain(s) in all given state(s) to any other given chain(s) in any other given state(s) for some given selection within a homo-oligomer. So, if you have an MD trajectory or NMR ensemble of a tertramer, for example, over 20 states this program could calculate the RMS values for residues 10-30 in chain A's state 17, against all of chain C. Or all states in all chains against each other.

See the notes in the code for usage.

The Code

<source lang="python">

  2. autoMultiFit.py -- Given a homo-oligomer in N-states, fit any combination of chains across states
  4. AUTHOR: Jason Vertrees
  5. DATE : 2009-11-02

import pymol from pymol import cmd

def autoMultiFit(sel, fromChain="*", fromState="*", toChain="*", toState="*", verbose=None): 

   """
   FUNCTION
     Given a homo-oligomer in N-states (say from MD), fit any
     combination of chains/selections across states. See Usage, Examples and Notes.

   USAGE
     autoMultiFit sel,  ..→
A Random PyMOL-generated Cover. See Covers.


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