Chimera Commands Index

addh options

Addh is the command-line implementation of AddH, which adds hydrogens to structures. See AddH for details on methodology, protonation states, and effects on radii.


Unlike the keywords of most commands, option keywords for addh can be truncated to unique strings. In addition, keyword case does not matter. Default values are indicated with bold. A vertical bar "|" designates mutually exclusive options. Synonyms for true: True, 1. Synonyms for false: False, 0.

hbond true|false
Whether to consider hydrogen bonding during hydrogen addition. This option increases calculation time and is still under development; use with caution.
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.

See also: delete