Difference between revisions of "Main Page"

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! Official Release
 
! Official Release
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| [https://pymol.org PyMOL v2.4 has been released] on May 20, 2020.
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| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
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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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! 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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! POSF
 
! POSF
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| [https://pymol.org/fellowship New PyMOL fellows announced for 2018-2019]
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| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
 
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! Tutorial
 
! Tutorial

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...

Colorbydisplacement

Type Python Script
Download colorbydisplacement.py
Author(s) Troels E. Linnet
License BSD
This code has been put under version control in the project Pymol-script-repo

Introduction

This script allows you to color two structures by distance displacement between an Open and Closed form of a protein, as calculated by PyMol's internal distance command. The pairwise distance is calculated between all-atoms. The distance displacement values are stored as B-factors of these residues, which are colored by a rainbow color spectrum, with blue specifying minimum and red indicating maximum.

Do keep in mind, all original B-factors values are overwritten!

There exist one version.
ColorByDisplacementAll is between All atoms in residues and is quite slow => 3-5 mins for a run. Ideal for sticks representation.

You have to specify which residues should be used in the alignment procedure, or it will take all residues as standard

V.2 is implemented the 2011.01.06 - Due to a bug in coloring.

Bug in code

A bug in the boolean operator of ..→

A Random PyMOL-generated Cover. See Covers.


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