CYANA Command: distances combine: Difference between revisions

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== Description ==
== Description ==


This command applies "constraint combination" for the distance
Applies “constraint combination” (Güntert, 2004; Herrmann et al., 2002) to the distance restraints that match the given ''selection''. 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. Constraint combination is normally applied to reduce the impact of erroneous distance restraints that may be generated in the initial cycles of combined automated NOESY assignment and structure calculation using the '''noeassign''' command.<br>
restraints that match the given '''selection'''. By default, the selection
Only distance restraints in the given support score range are combined.<br>
made in the most recent '''distances select''' command is used, or all
By default, or by setting '''combination=fourfour''', four new ambiguous distance restraints are formed from four selected individual restraints ''A'', ''B'', ''C'', ''D'' by combining the assignments from restraints ''A'' and ''B'', ''A'' and ''C'', ''A'' and ''D'', and ''B'' and ''C'', respectively. The assignments of restraint ''A'' are thus used in three of the new restraints, those from restraints ''B'' and ''C'' are used twice, and those from restraint ''D'' once. If the option 'equal' is set, then the four new restraints are instead formed from by combining the assignments from restraints ''A'' and ''C'', ''A'' and ''D'', ''B'' and ''D'', and ''B'' and ''C'', respectively, i.e. the assignments from of the each input restraints are used are used twice to form a combined restraint. Alternatively, by setting '''combination=twoone''', one new ambiguous distance restraint is formed from each pair of selected individual restraints ''A'' and ''B'' by combining their assignments.<br>
distance restraints if no selection has been made so far.
The input restraints that are selected for constraint combination are sorted according to their residue range ('''sort=level'''), their individual support score ('''sort=individual'''), or their residue-wise support score ('''sort=residue'''). The input restraints ''A'', ''B'', ''C'' and ''D'' in the case of 4-to-4 constraint combination are chosen from the first, second, third, and fourth quarter of the sorted list, respectively. In the case of 2-to-1 constraint combination, the restraints ''A'' and ''B'' are chosen from the first and second half of the sorted list, respectively.<br>
The upper distance bound ''u'' of the combined restraint is computed from the upper distance bounds ''u''<sub>1</sub>, ..., ''u''<sub>n</sub> of the restraints that are combined according to the '''distance''' parameter:


Constraint combination is normally applied to reduce the impact of
erroneous distance restraints that may be generated in the initial
cycles of combined automated NOESY assignment and structure calculation
using the '''noeassign''' command.


Only distance restraints with a support score in the range given by
  dsum   d<sup>-6</sup> sum: ''u''=(Σ''u''<sub>''i''</sub><sup>-6</sup> )<sup>-1/6</sup>
the '''support''' parameter are combined.
  dsumav  d<sup>-6</sup> average: ''u''=(1/nΣ''u''<sub>''i''</sub><sup>-6</sup>)<sup>-1/6</sup>
  dmax   Maximum: ''u''=max(''u''<sub>1</sub>, ..., ''u''<sub>n</sub>)


By default, or by setting '''combination=fourfour''', four new ambiguous
distance restraints are formed from four selected individual restraints
A, B, C, D by combining the assignments from restraints A and B,
A and C, A and D, and B and C, respectively. The assignments of
restraint A are thus used in three of the new restraints, those from
restraints B and C are used twice, and those from restraint D once. If
the option '''equal''' is set, then the four new restraints are instead
formed from by combining the assignments from restraints A and C,
A and D, B and D, and B and C, respectively, i.e. the assignments
from of the each input restraints are used are used twice to form a
combined restraint. Alternatively, by setting '''combination=twoone''',
one new ambiguous distance restraint is formed from wach pair of
selected individual restraints A and B by combining their assignments.


The input restraints that are selected for constraint combination
Normally, the individual restraints from which combined restraints are formed will be discarded. Optionally, the individual restraints can be kept with a (typically lower) relative weight given by the '''weightkeep''' parameter.
are sorted according to their residue range ('''sort=level'''), their
individual support score ('''sort=individual'''), or their residue-wise
support score ('''sort=residue'''). The input restraints A, B, C and D in
the case of 4-to-4 contraint combination are chosen from the first,
second, third, and fourth quarter of the sorted list, respectively. In
the case of 2-to-1 constraint combination, the restraints A and B are
chosen from the first and second half of the sorted list, respectively.
 
The upper distance bound u of the combined restraint is computed
from the upper distance bounds u_1,...,u_n of the restraints that
are combined according to the '''distance''' parameter:
 
  dsum      u = (u_1^-6 + ... + u_n^-6)^(-1/6)            d^-6 sum
  dsumav    u = ((u_1^-6 + ... + u_n^-6)/n)^(-1/6)d^-6    d^-6 average
  dmax      u = max(u_1,...,u_n)                          maximum
 
Normally, the individual restraints from which combined restraints
are formed will be discarded. Optionally, the individual restraints
can be kept with a (typically lower) relative weight given by the
'''weightkeep''' parameter.


Further reading:
Further reading:

Revision as of 13:52, 7 August 2009

Parameters

selection=string
(default: none)
distance=dsum|dsumav|dmax
(default: dsum)
support=real range
(default: 0.0..1.0E10)
weightkeep=real
(default: -1.0)
combination=fourfour|twoone
(default: fourfour)
sort=level|individual|residue
(default: level)
equal

Description

Applies “constraint combination” (Güntert, 2004; Herrmann et al., 2002) to the distance restraints that match the given selection. 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. Constraint combination is normally applied to reduce the impact of erroneous distance restraints that may be generated in the initial cycles of combined automated NOESY assignment and structure calculation using the noeassign command.
Only distance restraints in the given support score range are combined.
By default, or by setting combination=fourfour, four new ambiguous distance restraints are formed from four selected individual restraints A, B, C, D by combining the assignments from restraints A and B, A and C, A and D, and B and C, respectively. The assignments of restraint A are thus used in three of the new restraints, those from restraints B and C are used twice, and those from restraint D once. If the option 'equal' is set, then the four new restraints are instead formed from by combining the assignments from restraints A and C, A and D, B and D, and B and C, respectively, i.e. the assignments from of the each input restraints are used are used twice to form a combined restraint. Alternatively, by setting combination=twoone, one new ambiguous distance restraint is formed from each pair of selected individual restraints A and B by combining their assignments.
The input restraints that are selected for constraint combination are sorted according to their residue range (sort=level), their individual support score (sort=individual), or their residue-wise support score (sort=residue). The input restraints A, B, C and D in the case of 4-to-4 constraint combination are chosen from the first, second, third, and fourth quarter of the sorted list, respectively. In the case of 2-to-1 constraint combination, the restraints A and B are chosen from the first and second half of the sorted list, respectively.
The upper distance bound u of the combined restraint is computed from the upper distance bounds u1, ..., un of the restraints that are combined according to the distance parameter: 


 dsum	  d-6 sum: u=(Σui-6 )-1/6
 dsumav  d-6 average: u=(1/nΣui-6)-1/6 
 dmax	  Maximum: u=max(u1, ..., un)


Normally, the individual restraints from which combined restraints are formed will be discarded. Optionally, the individual restraints can be kept with a (typically lower) relative weight given by the weightkeep parameter.

Further reading:

  • Herrmann et al. J. Mol. Biol. 319, 209-227 (2002).
  • Guntert. Meth. Mol. Biol. 278, 353-378 (2004).

See also

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