CYANA Command: distances hbond: Difference between revisions

From CYANA Wiki
Jump to navigation Jump to search
m (1 revision)
 
Line 14: Line 14:
== Description ==
== Description ==


This command analyzes the selected structures with respect to potential
Searches the selected structures for potential hydrogen bonds and generates upper and lower distance bounds to restrain potential hydrogen bonds.<br>
hydrogen bonds and generates upper and lower distance bounds to
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.<br>
restrain potential hydrogen bonds.
A potential hydrogen bond must fulfill the following three criteria in at least the given number of  selected ''structures'':


Potential hydrogen bonds are searched between hydrogen atoms that
* The distance between the donor hydrogen and the acceptor must be shorter than the ''distance'' cutoff (in Å).
match the '''donors''' atom selection and other atoms that match the
* The angle at the donor hydrogen must be larger than the ''angledonor'' cutoff (in degrees).
'''acceptors''' atom selection. Only atoms that are declared as potential
* The angle(s) at the acceptor must be larger than the ''angleacceptor'' cutoff (in degrees).
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
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.<br>
in at least as many selected structures as defined by the '''structures'''
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.
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.

Revision as of 14:07, 7 August 2009

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: 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.

Retrieved from "https://cyana.org/w/index.php?title=CYANA_Command:_distances_hbond&oldid=6765"