Usage:
( hbonds | findhbond ) options

Usage:
( ~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). 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.

Option keywords for hbond (findhbond) can be truncated to unique strings; for example, intra but not inter would be acceptable, because both intermodel and interSubmodel 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.

selRestrict atom-spec|cross|both|any
Whether to limit H-bond detection to one of the following:

• those between atoms in atom-spec and the current selection; the specified atoms and the selection may overlap, but atom-spec will not overrule other restrictions (for example, if the specified atoms are in a different model than the selected atoms but intermodel is false, no H-bonds will be found). If atom-spec includes any spaces, it must be enclosed in single or double quote marks.
• cross - H-bonds with exactly one atom selected
• both - H-bonds with both atoms selected
• any - H-bonds with at least one atom selected

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.

intramodel true|false
Whether to look for H-bonds within models.

intermodel true|false
Whether to look for H-bonds between models.

interSubmodel true|false
Whether to look for H-bonds between submodels of the same model.

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 angstroms by default.

angleSlop tolerance
How much to relax the angle criteria if relax is true; tolerance is 20.0 degrees by default.

makePseudobonds true|false
Whether to create pseudobonds depicting the H-bonds found. These pseudobonds can be removed with the command ~hbonds or ~findhbond. The PseudoBond Panel can also be used to close the pseudobond group (named hydrogen bonds) or alter its display.

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.

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:

• simple - residue name, residue specifier, and atom name (for example, HIS 16.A ND1)
• command or command-line - command-line specifier (for example, :16.A@ND1)
• serial or serialnumber - atom serial number (for example, 126)

Model number will be included when multiple models are present. If namingStyle is not supplied, the Atomspec display style specified in the General 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.