CYANA Command: distances hbond

Parameters

donors=atom selection

(default: *)

acceptors=atom selection

(default: *)

distance=real

(default: 3.5)

angledonor=real

(default: 90.0)

angleacceptor=real

(default: 75.0)

structures=structure selection

(default: none)

weight=real

(default: 1.0)

ambiguous

append

Description

Searches the selected structures for 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 following three criteria in at least the given number of selected structures:

• The distance between the donor hydrogen and the acceptor must be shorter than the distance cutoff (in Å).
• The angle at the donor hydrogen must be larger than the angledonor cutoff (in degrees).
• The angle(s) at the acceptor must be larger than the angleacceptor cutoff (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 option is set.
The restraints consist of (unambiguous or ambiguous) upper distance limits of 2.0 Å between the donor hydrogen and the acceptor atom and of 3.0 Å 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 Å, respectively, are generated for the same distances. The relative weight of these distance restraints can be set. By default, unless the append option is set, these distance restraints replace all existing distance restraints.