CYANA Command: distances short

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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.

See also