CYANA Command: distances short - Revision history

Masayo: /* Parameters */

2009-08-13T13:56:50Z

Parameters

← Older revision		Revision as of 15:56, 13 August 2009
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	== Parameters ==		== Parameters ==

	; atoms=''~~string~~'': (default: *)		; atoms=''[[atom selection]]'': (default: *)
	; distance=''real'': (default: 9.0)		; distance=''real'': (default: 9.0)
	; structure		; structure
	; append		; append

	== Description ==		== Description ==

Masayo: /* Description */

2009-08-12T12:02:43Z

Description

← Older revision		Revision as of 14:02, 12 August 2009
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	== Description ==		== Description ==

	Identifies short-range interatomic distances between the selected ''atoms'' and stores them as distance restraints with zero weight, which are used for “network-anchoring” (Güntert, 2004; Herrmann et al., 2002) during automated NOESY cross peak assignment with the '''assign''' command.<br>		Identifies short-range interatomic distances between the selected ''atoms'' and stores them as distance restraints with zero weight, which are used for “network-anchoring” (Güntert, 2004; Herrmann et al., 2002) during automated NOESY cross peak assignment with the [[CYANA Commands: assign\|'''assign''']] command.<br>
	The upper bound is set to the maximal value that the short-range distance can take. Only short-range distances with a maximal distance shorter than the ''distance'' cutoff will be stored. If the option '''structure''' is set, then the maximum value of the distance is set to largest value found in the selected structures. Typically, these are a bundle of conformers that have no steric overlaps but otherwise random conformation. By default, i.e. if the option '''structure''' is not set, the maximum value of the distance is determined analytically for intraresidual and sequential distances that depend on up to two torsion angles, and extended to further intraresidual and sequential distances by repeated application of the triangle inequality. The absence or presence of stereospecific assignments is taken into account when determining the largest possible distance.<br>		The upper bound is set to the maximal value that the short-range distance can take. Only short-range distances with a maximal distance shorter than the ''distance'' cutoff will be stored. If the option '''structure''' is set, then the maximum value of the distance is set to largest value found in the selected structures. Typically, these are a bundle of conformers that have no steric overlaps but otherwise random conformation. By default, i.e. if the option '''structure''' is not set, the maximum value of the distance is determined analytically for intraresidual and sequential distances that depend on up to two torsion angles, and extended to further intraresidual and sequential distances by repeated application of the triangle inequality. The absence or presence of stereospecific assignments is taken into account when determining the largest possible distance.<br>
	By default, the short distances determined by this command will overwrite any distance restraints that are already in memory. If the option '''append''' is set, the short distances are instead appended to the current list of distance restraints.		By default, the short distances determined by this command will overwrite any distance restraints that are already in memory. If the option '''append''' is set, the short distances are instead appended to the current list of distance restraints.

Masayo: /* Description */

2009-08-07T13:35:53Z

Description

@@ Line 9: / Line 9: @@
 == Description ==
-This command identifies short-range interatomic distances between atoms
+Identifies short-range interatomic distances between the selected ''atoms'' and stores them as distance restraints with zero weight, which are used for “network-anchoring” (Güntert, 2004; Herrmann et al., 2002) during automated NOESY cross peak assignment with the '''assign''' command.<br>
-that match the selection and stores them as distance restraints with
+The upper bound is set to the maximal value that the short-range distance can take. Only short-range distances with a maximal distance shorter than the ''distance'' cutoff will be stored. If the option '''structure''' is set, then the maximum value of the distance is set to largest value found in the selected structures. Typically, these are a bundle of conformers that have no steric overlaps but otherwise random conformation.  By default, i.e.  if the option '''structure''' is not set, the maximum value of the distance is determined analytically for intraresidual and sequential distances that depend on up to two torsion angles, and extended to further intraresidual and sequential distances by repeated application of the triangle inequality. The absence or presence of stereospecific assignments is taken into account when determining the largest possible distance.<br>
-zero weight, which are used for "network-anchoring" during automated
+By default, the short distances determined by this command will overwrite any distance restraints that are already in memory. If the option '''append''' is set, the short distances are instead appended to the current list of distance restraints.
 == See also ==

Admin: 1 revision

2009-01-29T11:26:55Z

1 revision

New page

== Parameters ==

; atoms=''string'': (default: *)
; distance=''real'': (default: 9.0)
; structure
; append

== Description ==

This command identifies short-range interatomic distances between atoms
that match the selection and stores them as distance restraints with
zero weight, which are used for "network-anchoring" during automated
NOESY cross peak assignment with the '''assign''' command.

The upper bound is set to the maximal value that the short-range
distance can take. Only short-range distances with a maximal distance
shorter than the value of the '''distance''' parameter will be stored. If
the option '''structure''' is set, then the maximum value of the distance
is set to largest value found in the selected structures. Typically,
these are a bundle of conformers that have no steric overlaps but
otherwise random conformation. By default, i.e. if the option
'''structure''' is not set, the maximum value of the distance is determined
analytically for intraresidual and sequential distances that depend
on up to two dihedral angles, and extended to further intraresidual
and sequential distances by repeated application of the triangle
inequality. The absence or presence of stereospecific assignments is
taken into account when determining the largest possible distance.

By default, the short distances determined by this command will
overwrite any distance restraints that are already in memory. If the
option '''append''' is set, the short distances are instead append to
current list of distance restraints.

== See also ==

* [[assign]]
* [[noeassign]]