CYANA Command: distances check: Difference between revisions
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== Description == | == Description == | ||
Reports for each selected distance restraint a score (Mumenthaler & Braun, 1995) that indicates how well the distance restraint is embedded in the network of all (selected and unselected) distance restraints. Scores are computed only for distance restraints between atoms that are three or more residues apart from each other. For a given distance restraint the score is defined as the sum of the terms 1/((1+''k''<sub>1</sub>)(1+''k''<sub>2</sub>)) over all other distance restraints with both atoms in the same or directly neighboring residues as the two atoms of the restraint under consideration, where ''k''<sub>1</sub> and ''k''<sub>2</sub> denote the absolute residue index differences between the two first atoms and the two second atoms of the two restraints, respectively. A high score indicates that the distance restraint is well supported by other distance restraints. A low score is characteristic of "lonely" and therefore "dangerous" restraints with a potentially high impact on the calculated 3D structure. | |||
that indicates how well the distance restraint is embedded in the | |||
network of all (selected and unselected) distance restraints. Scores | |||
are computed only for distance restraints between atoms that are | |||
three or more residues apart from each other. | |||
or directly neighboring residues as the two atoms of the restraint | |||
under consideration, where | |||
differences between the two first atoms and the two second atoms of | |||
the two restraints. | |||
A high score | |||
by other restraints. A low score | |||
"dangerous" restraints with a potentially high impact on the calculated | |||
3D structure. | |||
Further reading: | Further reading: | ||
* Mumenthaler & Braun. J. Mol. Biol. 254, 465-480 (1995). | * Mumenthaler & Braun. J. Mol. Biol. 254, 465-480 (1995). | ||
Revision as of 14:33, 7 August 2009
Parameters
- selection=string
- (default: none)
Description
Reports for each selected distance restraint a score (Mumenthaler & Braun, 1995) that indicates how well the distance restraint is embedded in the network of all (selected and unselected) distance restraints. Scores are computed only for distance restraints between atoms that are three or more residues apart from each other. For a given distance restraint the score is defined as the sum of the terms 1/((1+k1)(1+k2)) over all other distance restraints with both atoms in the same or directly neighboring residues as the two atoms of the restraint under consideration, where k1 and k2 denote the absolute residue index differences between the two first atoms and the two second atoms of the two restraints, respectively. A high score indicates that the distance restraint is well supported by other distance restraints. A low score is characteristic of "lonely" and therefore "dangerous" restraints with a potentially high impact on the calculated 3D structure.
Further reading:
- Mumenthaler & Braun. J. Mol. Biol. 254, 465-480 (1995).