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Command: addh

addh  model-spec  [ hbond  true | false ] [ inIsolation  true | false ] [ metalDist  d ] [ template  true | false ]  residue-name-options

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

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. Hydrogens are named in accordance with the PDB standard if possible.

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 metalDist option specifies a distance between a heavy atom X and metal ion M (default 3.6 Å) within which to suppress adding a hydrogen to X if both of the following also apply:

The template option (default false) allows using idealized coordinates to discern atom types in nonstandard residues, instead of their actual coordinates in the structure. The idealized coordinates are looked up by residue name in the PDB Chemical Component Dictionary. Setting template true is useful for structures with poorly (structurally) determined ligands that could be mis-typed, potentially causing addition of the wrong number of hydrogens or hydrogens in incorrect positions.

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 unspecified (guess from local environment),
CYM negatively charged
all treated as unspecified

The atom types within these amino acids are ignored for hydrogen addition, so changing them manually to try to control hydrogen addition will have no effect.

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 / April 2021