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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... WriteSS == Overview == This script will write the secondary structural elements for each PDB file in some specified directory, for each alpha carbon in the protein, to an output text file. Residues without secondary structure definition will get a "." in the string. This is untested code and has little chance of working for anyone but me. Although, it does work for me. Instructions Copy the code to your machine Find FIXME in the code below and change "files" to either a glob like the one already there (for a whole directory) or a list with one element (for just one file). change the output filename. By default it's PDBCODE.ss. The Code <source lang="python"> import os import os.path import glob from pymol import cmd from pymol import stored from pymol import selector files = glob.glob("/tmp/thy_model/*.pdb") for file in files: pdbName = os.path.basename(file).split(".")[0] cmd.load(file, pdbName) outFile = open(pdbName + '.ss', 'wb') stored.ss = "" cmd.iterate( ..→

A Random PyMOL-generated Cover. See Covers.