The addh command adds hydrogen atoms to atomic models, as well as OXT atoms where missing from peptide C-termini. The corresponding tool is Add Hydrogens. See also: delete, build, hbonds, altlocs, addcharge, dockprep
Hydrogens are added to entire atomic model(s) even if only parts of models are specified. 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, and positioned to produce the expected bond lengths. An attempt is made to preserve coloring schemes, coloring the added hydrogens by element (white) and/or to match their bond partners.
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 3.95 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.
By default, if amino acids have standard residue names, each histidine sidechain will be protonated based on its local environment, whereas the sidechains of other residue types will be assigned protonation states reasonable at physiological pH, regardless of the local environment: negative aspartic acid and glutamic acid, positive arginine and lysine, and neutral cysteine and tyrosine. The following addh command 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 |
These names can be assigned to residues beforehand by text-editing the PDB file of the structure before it is opened, or by using the command setattr to change the name residue attribute. The atom types within these amino acids are ignored for hydrogen addition, so changing them to try to control hydrogen addition will have no effect.