CYANA Command: distances short: Difference between revisions
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== Parameters == | == Parameters == | ||
; atoms='' | ; atoms=''[[atom selection]]'': (default: *) | ||
; distance=''real'': (default: 9.0) | ; distance=''real'': (default: 9.0) | ||
; structure | ; structure | ||
; append | ; append | ||
== 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 [[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> | |||
zero weight, which are used for | 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. | ||
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 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 | |||
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 | |||
current list of distance restraints. | |||
== See also == | == See also == | ||
Latest revision as of 14:56, 13 August 2009
Parameters
- atoms=atom selection
- (default: *)
- distance=real
- (default: 9.0)
- structure
- append
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.
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.
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.