Chimera Commands Index

( hbonds | findhbond ) options

( ~hbonds | ~findhbond )

Hbonds (or findhbond) is the command-line implementation of FindHBond, which uses atom types and geometric criteria to identify possible hydrogen bonds (H-bonds). See the video mini-example. See also: addh, findclash, distance, PseudoBond Reader

It is not necessary for hydrogen atoms to be present. All potential H-bonding interactions fulfilling the criteria are shown. For example, even if it is not possible for a particular hydroxyl group to donate a hydrogen bond to two particular acceptors simultaneously, both possibilities will be displayed if the hydroxyl lacks an explicit hydrogen atom. If the hydroxyl group has an explicit hydrogen atom, however, only H-bonds compatible with the position of the hydrogen will be found. Consult the FindHBond manual page for more information on the method and criteria.

By default, hydrogen bonds are shown as pseudobonds. **If the endpoint atoms are subsequently moved relative to each other, the lines will “stretch” rather than disappearing, even if the atoms no longer meet the criteria for hydrogen bonding.** After such changes, the H-bonds should be updated by rerunning the calculation, or removed, e.g. with the command ~hbonds (or ~findhbond).


Option keywords for hbond (findhbond) 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.

makePseudobonds true | false
Whether to show the H-bonds as lines (a group of pseudobonds named hydrogen bonds). The pseudobonds will be drawn between the donor and acceptor atoms, or if hydrogens are present, between the hydrogens and acceptor atoms.
lineWidth width
Line width to use for pseudobonds depicting H-bonds (when in the wire draw mode); width is 1.0 pixels by default.
color colorname
Color to use for pseudobonds depicting H-bonds (but see also twoColors and slopColor). The default color is similar to cyan. Colorname can be none or any color name that specifies a single color.
showDist true | false
Whether to label the pseudobonds with the corresponding distances. The number of decimal points and whether the Å symbol is displayed can be set in the Distances tool (other settings in that tool will not affect hydrogen bonds pseudobonds, however).
selRestrict  atom-spec | cross | both | any
Whether to limit H-bond detection to one of the following: This option is off unless specified.
spec  atom-spec
Whether to restrict H-bond detection to a subset of the open molecule models. The entire model(s) containing the specified atoms will be considered. If atom-spec includes any spaces, it must be enclosed in single or double quote marks.
interSubmodel true | false
Whether to look for H-bonds between submodels of the same model.
intermodel true | false
Whether to look for H-bonds between models.
intramodel true | false
Whether to look for H-bonds within models.
intraMol true | false
Whether to include intramolecular H-bonds, where a molecule is defined as a covalently bonded set of atoms.
intraRes true | false
Whether to include intraresidue H-bonds.
cacheDA true | false
Whether to cache and reuse donor and acceptor information rather than regenerating it each time the command is used; useful for calculations on different conformations of the same structure. The default is true for a trajectory open in MD Movie (although a trajectory may not be recognized until more than one set of coordinates has been read), otherwise false.
relax true | false
Whether to relax the precise criteria for hydrogen bonding.
distSlop tolerance
How much to relax the distance criteria if relax is true; tolerance is 0.4 Å by default.
angleSlop tolerance
How much to relax the angle criteria if relax is true; tolerance is 20.0 degrees by default.
twoColors true | false
Whether to use different colors for H-bonds meeting and not meeting the precise criteria (i.e., whether a different color should be used for H-bonds outside the precise criteria but within the tolerance values).
slopColor colorname
If twoColors is true, the color to use for depicting H-bonds not meeting the precise criteria but within the tolerance values. The default color is similar to orange. Colorname can be none or any color name that specifies a single color.
reveal true | false
Whether to turn on the display of residues containing an H-bonding atom if that atom is not displayed initially. (By default, if the atom on either end of a pseudobond representing an H-bond is not shown, the pseudobond itself is not shown, although it still exists; displaying the atom allows the H-bond to be shown.)
retainCurrent true | false
Whether to keep the pseudobonds depicting a previously determined set of H-bonds through a subsequent round of detection (as opposed to replacing the old with the new).
saveFile file
Whether to save H-bond information to a file (this option is off unless specified). The information includes donor and acceptor atom specifications (see namingStyle), donor-acceptor distances, and when hydrogens are present, hydrogen atom specifications and hydrogen-acceptor distances. File is the output file name/pathname; if it includes spaces, it must be enclosed in single or double quote marks. If file is browse or browser, a dialog for saving the file will appear (unless the word is enclosed in quotes, which would generate an output file by that name).
log true | false
Whether to write H-bond information (as described above for saveFile) to the Reply Log.
namingStyle simple | command | serial
How to describe atoms in H-bond information written to a file or the log: Model number will be included when multiple models are present. If namingStyle is not supplied, the Atomspec display style specified in the Labels preferences will be used.
batch true | false
Whether to suppress certain errors; useful for no-GUI batch processing. Currently, the only error suppressed when batch is true is that which arises if no atoms are selected when selRestrict is specified.