Addh adds hydrogens to molecules, as well as OXT atoms where missing from peptide C-termini. It is the command-line implementation of AddH. Chimera uses atom and residue names, or if these are not "standard," atomic coordinates, to determine connectivity and atom types; the atom types are then used to determine the number of hydrogens to be added and their positions. The positions of pre-existing atoms are not changed, but any lone pairs and unidentifiable-element atoms are deleted. If any atoms cannot be assigned a type, a dialog will appear. It is necessary to click on the line for each unassigned atom and then indicate its proper substituent geometry and number of substituents.
Added hydrogens will be colored the element color (default white) if the attached atom is colored by element, otherwise to match the attached atom.
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 glutamic acid and aspartic acid, positive lysine and arginine, and neutral cysteine and tyrosine. Alternative protonation states of histidine, glutamic acid, aspartic acid, lysine, and cysteine can be specified with special residue names in the input coordinate file (see the options). To specify the protonation states of individual residues interactively, use the AddH graphical interface instead of the addh command.
See the AddH manual page for details including bond lengths and effects on radii. See also: delete, hbonds, addcharge, pdb2pqr, vina, Dock Prep
Option keywords for addh can be truncated to unique strings and their case does not matter. A vertical bar "|" designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.
Whether to restrict hydrogen addition to a subset of the open molecule models. Hydrogens will be added to the entire model(s) containing the specified atoms. If atom-spec includes any spaces, it must be enclosed in single or double quote marks.
inIsolation true | false
Whether hydrogen placement should be affected by atoms within the same model only. Otherwise, other models in the vicinity (except submodels of the same model) may affect hydrogen placement, regardless of whether they were designated for hydrogen addition.
hbond true | false
Hydrogens are placed based on the types of the existing atoms and to avoid clashes; this option controls whether H-bond formation should also be considered. Considering H-bonds increases calculation time, and the method is still under development. Even when hbond is true, hydrogen positions are not energy-minimized, and a globally optimal network in terms of the number of H-bonds or total H-bonding energy is not necessarily found. Both intra- and inter-model hydrogen bonds are considered, including interactions with models to which hydrogens are not being added (as in FindHBond when the scope of the calculation is set to both).
useHisName true | false
Whether to use residue names for histidine to determine which sidechain nitrogens should be protonated: the δ-nitrogen in residues named HID, the ε-nitrogen in HIE, and both nitrogens in HIP. Residues named HIS will be treated as unspecified, and may end up with either or both sidechain nitrogens protonated depending on the local environment and whether H-bonds are being considered (whether hbond is true). If useHisName is false, all histidine residues will be treated as unspecified regardless of which of the above residue names are used.
useGluName true | false
Whether to use residue names for glutamic acid to determine sidechain charge state: GLU negatively charged and GLH neutral (OE2-protonated). If false, all glutamic acid sidechains will be made negatively charged regardless of which of the above residue names are used.
useAspName true | false
Whether to use residue names for aspartic acid to determine sidechain charge state: ASP negatively charged and ASH neutral (OD2-protonated). If false, all aspartic acid sidechains will be made negatively charged regardless of which of the above residue names are used.
useLysName true | false
Whether to use residue names for lysine to determine sidechain charge state: LYS positively charged and LYN neutral. If false, all lysine sidechains will be made positively charged regardless of which of the above residue names are used.
useCysName true | false
Whether to use residue names for cysteine to determine sidechain charge state: CYS treated as unspecified and CYM negatively charged. If false, all cysteine sidechains will be treated as unspecified regardless of which of the above residue names are used.