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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
Official Release PyMOL v2.3 has been released on February 11, 2019.
POSF New PyMOL fellows announced for 2018-2019
Tutorial Plugins Tutorial updated for PyQt5
New Plugin ProBiS H2O is a new plugin for identification of conserved waters in protein structures.
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...

H Add

h_add uses a primitive algorithm to add hydrogens onto a molecule.

Usage and Algorithm Notes

PyMOL fills missing valences but does no optimization of hydroxyl rotamers. Also, many crystal structures have bogus or arbitrary ASN/GLN/HIS orientations. Getting the proper amide rotamers and imidazole tautomers & protonation states assigned is a nontrivial computational chemistry project involving electrostatic potential calculations and a combinatorial search. There's also the issue of solvent & counter-ions present in systems like aspartyl proteases with adjacent carboxylates .

Accessing Through GUI



# normal usage
h_add (selection)

# API usage
cmd.h_add( string selection="(all)" )

see also H_Fill

A Random PyMOL-generated Cover. See Covers.