CYANA Command: distances split: Difference between revisions

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== Description ==
== Description ==


This command can replace ambiguous distance restraints that match
Splits suitable ambiguous distance restraints that match the given ''selection'' into several unambiguous distance restraints. By default, the selection made in the most recent '''distances select''' command is used, or all distance restraints if no selection has been made so far. Each of the new distance restraints will be assigned uniquely to one of the multiple assignments of the ambiguous input restraint. The upper distance bound u' of a new restraint is obtained from the upper bound u of the corresponding ambiguous input restraint according to the formula
the given '''selection''' by several unambiguous distance restraints. By
default, the selection made in the most recent '''distances select'''
command is used, or all distance restraints if no selection has been
made so far. Each of the new distance restraints will be assigned
uniquely to one of the multiple assignments of the ambiguous input
restraint.


The upper distance bound u''' of a new restraint is obtained from the
  u' = u [1 + f ((V'/V)<sup>(-1/n)</sup> - 1)],
upper bound u of the corresponding ambiguous input restraint according
to the formula


  u''' = u * (1 + f * ((V'''/V)^(-1/n) - 1)),
where ''f''=''extension'', ''n''=''exponent'', and V'/V is the fraction of the total NOESY cross peak volume of the original ambiguous restraint that originates from the single assignment of the new restraint.<br>
 
This volume contribution is computed for each selected structure by assuming a ''r''<sup>-6</sup> distance-to-volume relationship. The average over all conformers of these volume contributions is used for the fraction V'/V. Only assignments for which V'/V>''keep'' are kept to generate an unambiguous distance restraint, others are discarded.
where f and n denote the values of the '''extension''' and '''exponent'''
parameters, respectively, and V'''/V is the fraction of the total
NOESY cross peak volume of the original ambiguous restraint that
originates from the single assignment of the new restraint. This volume
contribution is computed for each selected structure by assuming an
r^-6 distance-to-volume relationship. The average over all conformers
of these volume contributions is used for the fraction V'''/V. Only those
assignments for which V'''/V exceeds the threshold given by the '''keep'''
parameter are kept to generate an unambiguous distance restraint,
others are discarded.

Revision as of 15:46, 7 August 2009

Parameters

selection=string
(default: none)
keep=real
(default: 0.25)
exponent=real
(default: 6.0)
extension=real
(default: 1.0)

Description

Splits suitable ambiguous distance restraints that match the given selection into several unambiguous distance restraints. By default, the selection made in the most recent distances select command is used, or all distance restraints if no selection has been made so far. Each of the new distance restraints will be assigned uniquely to one of the multiple assignments of the ambiguous input restraint. The upper distance bound u' of a new restraint is obtained from the upper bound u of the corresponding ambiguous input restraint according to the formula 

 u' = u [1 + f ((V'/V)(-1/n) - 1)],

where f=extension, n=exponent, and V'/V is the fraction of the total NOESY cross peak volume of the original ambiguous restraint that originates from the single assignment of the new restraint.
This volume contribution is computed for each selected structure by assuming a r-6 distance-to-volume relationship. The average over all conformers of these volume contributions is used for the fraction V'/V. Only assignments for which V'/V>keep are kept to generate an unambiguous distance restraint, others are discarded.

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