H Add

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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