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News & Updates Official Release PyMOL v2.4 has been released on May 20, 2020. Python 3 New Python 3 compatibility guide for scripts and plugins POSF New PyMOL fellows announced for 2018-2019 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... Super super aligns two selections. It does a sequence-independent (unlike align) structure-based dynamic programming alignment followed by a series of refinement cycles intended to improve the fit by eliminating pairing with high relative variability (just like align). super is more robust than align for proteins with low sequence similarity. Usage See align command. Caveats Alternative Conformations: If super ever tells you no matched atoms, then instead of super p1, p2 try super p1 & alt A+'', p2 & alt B+'' User Scripts Write rmsd to file pymol_rmsd_test.pml reinitialize fetch 1F9J, async=0 fetch 1YX5, async=0 extract 1F9J_A, 1F9J and chain A extract 1YX5_B, 1YX5 and chain B test=cmd.super("1F9J_A","1YX5_B") python writefile=open("rmsd_file.txt","a") writefile.write(' '.join('%s' % x for x in test)) writefile.write('\n') writefile.close() python end In ..→

A Random PyMOL-generated Cover. See Covers.