CYANA Command: distances hbond - Revision history

Masayo: /* Parameters */

2009-08-13T12:04:26Z

Parameters

← Older revision		Revision as of 14:04, 13 August 2009
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	== Parameters ==		== Parameters ==

	; donors=''~~string~~'': (default: *)		; donors=''[[atom selection]]'': (default: *)
	; acceptors=''~~string~~'': (default: *)		; acceptors=''[[atom selection]]'': (default: *)
	; distance=''real'': (default: 3.5)		; distance=''real'': (default: 3.5)
	; angledonor=''real'': (default: 90.0)		; angledonor=''real'': (default: 90.0)
	; angleacceptor=''real'': (default: 75.0)		; angleacceptor=''real'': (default: 75.0)
	; structures=''~~integer~~'': (default: ''none'')		; structures=''[[structure selection]]'': (default: ''none'')
	; weight=''real'': (default: 1.0)		; weight=''real'': (default: 1.0)
	; ambiguous		; ambiguous
	; append		; append

	== Description ==		== Description ==

Masayo: /* Description */

2009-08-07T13:07:03Z

Description

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 == 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).
-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.

Admin: 1 revision

2009-01-29T11:26:55Z

1 revision

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== 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 ==

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.