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Command: addh

addh  model-spec  hbond  true | false ] inIsolation  true | false ]  other-options

The addh command adds hydrogen atoms to atomic models, as well as OXT atoms where missing from peptide C-termini. See also: delete, hbonds

Hydrogens are added to entire atomic model(s) even if only parts of models are specified. Placement is based on atom types and to avoid clashes, if possible. The positions of pre-existing atoms are not changed, but any lone pairs and atoms of unidentifiable element are deleted.

Specifying hbond false is currently required:
The hbond option (default true) controls whether H-bond formation should also be considered. Considering H-bonds increases calculation time and may not produce a globally optimal network of H-bonds.

The inIsolation option (default true) indicates using only the atoms within the same model. Otherwise, other models in the vicinity (except sibling submodels of the same model) may affect hydrogen placement, even if the other models were not designated for hydrogen addition. Sibling submodels of the same model (e.g., #1.1, #1.2, #1.3, ...) are always treated in isolation from one another, even if this option is false.

The remaining options allow alternative protonation states of certain amino acids to be specified with special residue names:

option true (default) false
useHisName HIS unspecified (guess from local environment),
HID δ-nitrogen protonated, HIE ε-nitrogen protonated,
HIP both sidechain nitrogens protonated
all treated as unspecified
useAspName ASP negatively charged, ASH neutral (OD2-protonated) all negatively charged
useGluName GLU negatively charged, GLH neutral (OE2-protonated) all negatively charged
useLysName LYS positively charged, LYN neutral all positively charged
useCysName CYS neutral, CYM negatively charged all neutral

An attempt is made to preserve coloring schemes, coloring the added hydrogens by element (white) and/or to match their bond partners.

UCSF Resource for Biocomputing, Visualization, and Informatics / October 2017