Hbonds (or findhbond) is the command-line implementation of FindHBond, which uses atom types and geometric criteria to identify possible hydrogen bonds (H-bonds). 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. ~Hbonds (or ~findhbond) removes these pseudobonds.Option keywords for hbond (findhbond) can be truncated to unique strings; for example, intra but not inter would be acceptable, because both intermodel and interSubmodels start with inter. In addition, keyword 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.
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.
intramodel true|false
Whether to look for H-bonds within models.
intermodel true|false
Whether to look for H-bonds between models.
interSubmodels true|false
Whether to look for H-bonds between submodels of the same model.
selRestrict set
Consider only H-bonds with atoms in the current selection (this option is off unless specified). The set can be:
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 slopColor). The default color is similar to cyan. Colorname can be none or any color name that specifies a single color.
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 angstroms 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.
saveFile file
Whether to save H-bond information in a file (this option is off unless specified). The information includes donor and acceptor atom specifications (see namingStyle), donor-acceptor distances, and hydrogen-acceptor distances (when hydrogens are present). 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 to the Reply Log. The information includes donor and acceptor atom specifications (see namingStyle), donor-acceptor distances, and hydrogen-acceptor distances (when hydrogens are present).
namingStyle simple|osl
How to specify atoms in H-bond information written to a file or the log: simple (for example, #0 PHE 16 CD1) or osl (command-line specifier, for example, #0:16@CD1). In the absence of this keyword, the Atomspec display style specified in the General preferences will be used.
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.)
makePseudobonds true|false
Whether to create pseudobonds depicting the H-bonds found.
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).
batch true|falseSee also: addh, distance, findclash, FindHBond, the PseudoBond Panel
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.