CYANA Command: distances split - Revision history

Masayo: /* Parameters */

2009-08-13T10:05:22Z

Parameters

← Older revision		Revision as of 12:05, 13 August 2009
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	== Parameters ==		== Parameters ==

	; selection=''~~string~~'': (default: ''none'')		; selection=''[[distance restraint selection]]'': (default: ''none'')
	; keep=''real'': (default: 0.25)		; keep=''real'': (default: 0.25)
	; exponent=''real'': (default: 6.0)		; exponent=''real'': (default: 6.0)

Masayo: /* Description */

2009-08-12T12:01:27Z

Description

← Older revision		Revision as of 14:01, 12 August 2009
Line 9:		Line 9:
	== Description ==		== 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		Splits suitable ambiguous distance restraints that match the given ''selection'' into several unambiguous distance restraints. 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. 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)<sup>(-1/n)</sup> - 1)],		u' = u [1 + f ((V'/V)<sup>(-1/n)</sup> - 1)],

Masayo: /* Description */

2009-08-07T13:46:19Z

Description

@@ Line 9: / Line 9: @@
 == 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 upper distance bound u''' of a new restraint is obtained from the
+  u' = u [1 + f ((V'/V)<sup>(-1/n)</sup> - 1)],
-  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.

Admin: 1 revision

2009-01-29T11:26:55Z

1 revision

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== Parameters ==

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

== Description ==

This command can replace ambiguous distance restraints that match
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
upper bound u of the corresponding ambiguous input restraint according
to the formula

u''' = u * (1 + f * ((V'''/V)^(-1/n) - 1)),

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.