https://cyana.org/w/index.php?action=history&feed=atom&title=CYANA_Commands%3A_distances_split 2026-04-09T19:14:25Z Revision history for this page on the wiki MediaWiki 1.45.1 https://cyana.org/w/index.php?title=CYANA_Commands:_distances_split&diff=4540&oldid=prev 2009-01-28T23:35:41Z

<p>1 revision</p> <p><b>New page</b></p><div><br /> == Parameters ==<br /> <br /> ; selection=&#039;&#039;string&#039;&#039;: (default: &#039;&#039;none&#039;&#039;)<br /> ; keep=&#039;&#039;real&#039;&#039;: (default: 0.25)<br /> ; exponent=&#039;&#039;real&#039;&#039;: (default: 6.0)<br /> ; extension=&#039;&#039;real&#039;&#039;: (default: 1.0)<br /> <br /> == Description ==<br /> <br /> This command can replace ambiguous distance restraints that match<br /> the given &#039;&#039;&#039;selection&#039;&#039;&#039; by several unambiguous distance restraints. By<br /> default, the selection made in the most recent &#039;&#039;&#039;distances select&#039;&#039;&#039;<br /> command is used, or all distance restraints if no selection has been<br /> made so far. Each of the new distance restraints will be assigned<br /> uniquely to one of the multiple assignments of the ambiguous input<br /> restraint.<br /> <br /> The upper distance bound u&#039;&#039;&#039; of a new restraint is obtained from the<br /> upper bound u of the corresponding ambiguous input restraint according<br /> to the formula<br /> <br /> u&#039;&#039;&#039; = u * (1 + f * ((V&#039;&#039;&#039;/V)^(-1/n) - 1)),<br /> <br /> where f and n denote the values of the &#039;&#039;&#039;extension&#039;&#039;&#039; and &#039;&#039;&#039;exponent&#039;&#039;&#039;<br /> parameters, respectively, and V&#039;&#039;&#039;/V is the fraction of the total<br /> NOESY cross peak volume of the original ambiguous restraint that<br /> originates from the single assignment of the new restraint. This volume<br /> contribution is computed for each selected structure by assuming an<br /> r^-6 distance-to-volume relationship. The average over all conformers<br /> of these volume contributions is used for the fraction V&#039;&#039;&#039;/V. Only those<br /> assignments for which V&#039;&#039;&#039;/V exceeds the threshold given by the &#039;&#039;&#039;keep&#039;&#039;&#039;<br /> parameter are kept to generate an unambiguous distance restraint,<br /> others are discarded.</div>

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