ChimeraX docs icon

Tool: H-Bonds

The H-Bonds tool uses atom types and geometric criteria to identify hydrogen bonds (H-bonds). It is also implemented as the hbonds command. See also: H-bond-related features, Add Hydrogens, Clashes/Contacts, Distances, addh, interfaces, Molecule Display icons: , Protein-Ligand Binding Sites tutorial

H-Bonds can be opened from the Structure Analysis section of the Tools menu and manipulated like other panels (more...).

It is not necessary to add hydrogens first, as their possible positions will be inferred if they are missing. The number of H-bonds found is reported in the Log. This number includes all H-bonds consistent with the chosen options, even if the H-bonds could not coexist simultaneously. For example, both donor-acceptor and acceptor-donor H-bonds could be found between the the same pair of atoms, and a hydroxyl group could be found to donate a hydrogen bond to two different acceptors even if only one or the other could be the acceptor at a given time. If the hydroxyl group has an explicit hydrogen atom, however, only H-bonds compatible with the position of the hydrogen will be found.

Clicking Apply (or OK, which also dismisses the dialog) runs the calculation. Several of the dialog settings are remembered as preferences when the calculation is run. Clicking Reset restores the dialog to factory default settings.

UCSF Resource for Biocomputing, Visualization, and Informatics / September 2022