https://cyana.org/w/index.php?action=history&feed=atom&title=CYANA_Commands%3A_distances_shortCYANA Commands: distances short - Revision history2026-04-09T19:16:31ZRevision history for this page on the wikiMediaWiki 1.45.1https://cyana.org/w/index.php?title=CYANA_Commands:_distances_short&diff=4538&oldid=prevAdmin: 1 revision2009-01-28T23:35:41Z<p>1 revision</p>
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== Parameters ==<br />
<br />
; atoms=''string'': (default: *)<br />
; distance=''real'': (default: 9.0)<br />
; structure <br />
; append <br />
<br />
== Description ==<br />
<br />
This command identifies short-range interatomic distances between atoms<br />
that match the selection and stores them as distance restraints with<br />
zero weight, which are used for "network-anchoring" during automated<br />
NOESY cross peak assignment with the '''assign''' command.<br />
<br />
The upper bound is set to the maximal value that the short-range<br />
distance can take. Only short-range distances with a maximal distance<br />
shorter than the value of the '''distance''' parameter will be stored. If<br />
the option '''structure''' is set, then the maximum value of the distance<br />
is set to largest value found in the selected structures. Typically,<br />
these are a bundle of conformers that have no steric overlaps but<br />
otherwise random conformation. By default, i.e. if the option<br />
'''structure''' is not set, the maximum value of the distance is determined<br />
analytically for intraresidual and sequential distances that depend<br />
on up to two dihedral angles, and extended to further intraresidual<br />
and sequential distances by repeated application of the triangle<br />
inequality. The absence or presence of stereospecific assignments is<br />
taken into account when determining the largest possible distance.<br />
<br />
By default, the short distances determined by this command will<br />
overwrite any distance restraints that are already in memory. If the<br />
option '''append''' is set, the short distances are instead append to<br />
current list of distance restraints.<br />
<br />
== See also ==<br />
<br />
* [[assign]]<br />
* [[noeassign]]</div>Admin