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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... MakeVinaCommand = Overview = Vina is a new, very fast, molecular docking program, written by Oleg Trott. In order to run Vina, you should have MGLTools1.5.4 installed (you need prepare_receptor4.py and prepare_ligand4.py). But, you don't need MGLTools for this script to run. To run Vina it needs to know the center of the protein and also its extents (size in XYZ directions). We can easily do this with PyMOL. Requirements: COM -- simple script to get the center of mass of a selection Todo: Commandline options Robustness to vagaries of input Usage & Help Usage pymol -cq ./makeVinaCommandFromProtein.py proteinFile ligandFile For high-throughput screening, where we compare each ligand to each protein, I typically wrap the script in a for-loop like: <source lang="bash"> foreach protein in my proteins directory for protein in proteinsDir/*; do # foreach ligand in my ligands directory for ligand in ligandsDir/*; do; # make a ..→

A Random PyMOL-generated Cover. See Covers.