CYANA Command: distances combine - Revision history

Masayo: /* Parameters */

2009-08-13T10:00:08Z

Parameters

← Older revision		Revision as of 12:00, 13 August 2009
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	== Parameters ==		== Parameters ==

	; selection=''~~string~~'': (default: ''none'')		; selection=''[[distance restraint selection]]'': (default: ''none'')
	; distance=dsum\|dsumav\|dmax: (default: dsum)		; distance=dsum\|dsumav\|dmax: (default: dsum)
	; support=''real range'': (default: 0.0..1.0E10)		; support=''real range'': (default: 0.0..1.0E10)
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	; combination=fourfour\|twoone: (default: fourfour)		; combination=fourfour\|twoone: (default: fourfour)
	; sort=level\|individual\|residue: (default: level)		; sort=level\|individual\|residue: (default: level)
	; equal		; equal

	== Description ==		== Description ==

Masayo: /* Description */

2009-08-12T12:09:36Z

Description

← Older revision		Revision as of 14:09, 12 August 2009
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	== Description ==		== 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\|'''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 [[CYANA Macro: noeassign\|'''noeassign''']] command.<br>		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 [[CYANA Commands: distances select\|'''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 [[CYANA Macro: noeassign\|'''noeassign''']] command.<br>
	Only distance restraints in the given support score range are combined.<br>		Only distance restraints in the given support score range are combined.<br>
	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>		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>

Masayo: /* See also */

2009-08-12T08:32:31Z

Masayo: /* Description */

2009-08-12T08:30:51Z

Description

← Older revision		Revision as of 10:30, 12 August 2009
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	== Description ==		== 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\|'''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\|'''noeassign''']] command.<br>		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\|'''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 [[CYANA Macro: noeassign\|'''noeassign''']] command.<br>
	Only distance restraints in the given support score range are combined.<br>		Only distance restraints in the given support score range are combined.<br>
	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>		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>

Masayo: /* Description */

2009-08-12T08:24:46Z

Description

← Older revision		Revision as of 10:24, 12 August 2009
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	== Description ==		== 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.<br>		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\|'''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\|'''noeassign''']] command.<br>
	Only distance restraints in the given support score range are combined.<br>		Only distance restraints in the given support score range are combined.<br>
	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>		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>
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	dsum d<sup>-6</sup> sum: ''u''=(Σ''u''<sub>''i''</sub><sup>-6</sup> )<sup>-1/6</sup>		'''dsum''' ''d''<sup>-6</sup> sum: ''u''=(Σ''u''<sub>''i''</sub><sup>-6</sup> )<sup>-1/6</sup>
	dsumav d<sup>-6</sup> average: ''u''=(1/nΣ''u''<sub>''i''</sub><sup>-6</sup>)<sup>-1/6</sup>		'''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>)		'''dmax''' Maximum: ''u''=max(''u''<sub>1</sub>, ..., ''u''<sub>n</sub>)

Masayo: /* Description */

2009-08-07T12:52:27Z

Description

@@ Line 12: / Line 12: @@
 == 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>
-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>
-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.
 Further reading:

Admin: 1 revision

2009-01-29T11:26:55Z

1 revision

New page

== 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 ==

This command applies "constraint combination" for 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 with a support score in the range given by
the '''support''' parameter 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 wach 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 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:

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

== See also ==

* [[noeassign]]

← Older revision		Revision as of 10:32, 12 August 2009
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	== See also ==		== See also ==

	* [[noeassign]]		* [[CYANA Macro: noeassign\|'''noeassign''']]