CYANA Command: couplings make: Difference between revisions
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== Parameters == | == Parameters == | ||
; first='' | ; first=''[[atom selection]]'': (required) | ||
; second='' | ; second=''[[atom selection]]'': (required) | ||
; value=''real'': (default: 1.0) | ; value=''real'': (default: 1.0) | ||
; tolerance=''real'': (default: 1.0) | ; tolerance=''real'': (default: 1.0) | ||
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== Description == | == Description == | ||
Makes new scalar coupling constant restraints. Scalar coupling constant restraints are added between atoms selected by the ''first'' and ''second'' atom selections, respectively, provided that the two atoms are separated by three covalent bonds, of which the second must be a rotatable bond. The scalar coupling constant ''value'', its ''tolerance'', relative ''weight'', and the Karplus curve can be set. The command can also be used to simulate scalar coupling constant restraints on the basis of a given structure: If the '''value''' parameter is not given, the scalar coupling constant value of the new restraints will be set to the average value obtained from the selected conformers using the given Karplus curve. Karplus curves must be given as ''A'''''+'''''B'''''*cos(d)+'''''C'''''*cos(d)**2''', where ''A'', ''B'' and ''C'' are real numbers, and '''d''' denotes the value of the torsion angle formed by the two scalar coupled atoms. | |||
restraints are added between atoms selected by the | |||
atom selections, respectively. The scalar coupling constant | |||
The command can also be used to simulate scalar coupling constant | |||
restraints on the basis of a given structure: If the '''value''' parameter | |||
is not given, | |||
restraints will be to the average value obtained from the selected | |||
conformers using the given Karplus curve. | |||
Karplus curves must be | |||
where A, B and C are real numbers, and d denotes the value of the | |||
torsion angle formed by the two scalar coupled atoms. | |||
Latest revision as of 15:46, 13 August 2009
Parameters
- first=atom selection
- (required)
- second=atom selection
- (required)
- value=real
- (default: 1.0)
- tolerance=real
- (default: 1.0)
- weight=real
- (default: 1.0)
- karpluscurve=string
- (default: none)
Description
Makes new scalar coupling constant restraints. Scalar coupling constant restraints are added between atoms selected by the first and second atom selections, respectively, provided that the two atoms are separated by three covalent bonds, of which the second must be a rotatable bond. The scalar coupling constant value, its tolerance, relative weight, and the Karplus curve can be set. The command can also be used to simulate scalar coupling constant restraints on the basis of a given structure: If the value parameter is not given, the scalar coupling constant value of the new restraints will be set to the average value obtained from the selected conformers using the given Karplus curve. Karplus curves must be given as A+B*cos(d)+C*cos(d)**2, where A, B and C are real numbers, and d denotes the value of the torsion angle formed by the two scalar coupled atoms.