Chimera Commands Index

addh options

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 are colored the element color (default white) if the attached atom is colored by element, otherwise the same as the attached atom.

See the AddH manual page for details including bond lengths and effects on radii.


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.

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. To specify interactively the protonation state of each histidine, use the AddH graphical interface instead of the command addh. For other types of residues, addh attempts to achieve protonation states reasonable at physiological pH.
spec atom-spec
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. Regardless of whether they are specified for hydrogen addition, other models in the vicinity will affect hydrogen placement; if such interactions are not desired, the other models should be closed before hydrogens are added. Different submodels of the same model will not affect each other, however.

See also: delete, hbonds, addcharge, AddH,