6CYANA: distances hbond - CYANA command

Parameters: donors=<string>                (default: *)
            acceptors=<string>             (default: *)
            distance=<real>                (default: 3.5)
            angledonor=<real>              (default: 90.0)
            angleacceptor=<real>           (default: 75.0)
            structures=<integer>           (default: <blank>)
            weight=<real>                  (default: 1.0)
            ambiguous
            append

This command analyzes the selected structures with respect to potential
hydrogen bonds and generates upper and lower distance bounds to
restrain potential hydrogen bonds.

Potential hydrogen bonds are searched between hydrogen atoms that
match the 'donors' atom selection and other atoms that match the
'acceptors' atom selection. Only atoms that are declared as potential
hydrogen donors or acceptors in the 'ATOMTYPES' entry of the residue
library are taken into consideration.

A potential hydrogen bond must fulfill the three following criteria
in at least as many selected structures as defined by the 'structures'
parameter:

 - The distance between the donor hydrogen and the acceptor must be
   shorter than the cutoff given by the 'distance' parameter (in Angstrom).
 - The angle at the donor hydrogen must be larger than the cutoff given
   by the 'angledonor' parameter (in degrees).
 - The angle(s) at the acceptor must be larger than the cutoff given
   by the 'angleacceptor' parameter (in degrees).

Unambiguous hydrogen bond restraints are generated, if a donor hydrogen
is involved in a single potential hydrogen bond. If several potential
hydrogen bonds can be found for a donor hydrogen, then ambiguous
hydrogen bond restraints are generated only if the 'ambiguous'
optionm is set.

The restraints consist of (unambiguous or ambiguous) upper distance
limits of 2.0 Angstrom between the donor hydrogen and the acceptor
atom and of 3.0 Angstrom between the acceptor atom and the atom that
is covalently bound to the donor hydrogen. Unambiguous lower distance
limits of 1.8 and 2.7 Angstrom, respectively, are generated for the
same distances. The relative weight of these distance restraints can
be set with the 'weight'parameter. By default, unless the 'append'
option is set, these distance restraints replace all existing distance
restraints.
