https://cyana.org/w/index.php?action=history&feed=atom&title=CYANA_Commands%3A_atoms_calibrate 2026-04-18T21:39:25Z Revision history for this page on the wiki MediaWiki 1.45.1 https://cyana.org/w/index.php?title=CYANA_Commands:_atoms_calibrate&diff=4478&oldid=prev 2009-01-28T23:35:40Z

<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 /> ; peaklists=&#039;&#039;integer range&#039;&#039;: (default: 1..1)<br /> ; constant=&#039;&#039;real&#039;&#039;: (default: -1.0)<br /> ; dref=&#039;&#039;real&#039;&#039;: (default: 3.4)<br /> ; volcut=&#039;&#039;real&#039;&#039;: (default: 0.66)<br /> <br /> == Description ==<br /> <br /> Command to set the calibration constant of the atoms matched by<br /> the selection &#039;&#039;string&#039;&#039; for the chosen &#039;&#039;peaklists&#039;&#039;. By default, the<br /> selection made in the most recent &#039;&#039;&#039;atoms select&#039;&#039;&#039; command is used,<br /> or all atoms if no selection has been made so far. The calibration<br /> constant can either be set explicitly to a given positive &#039;&#039;constant&#039;&#039;,<br /> or it can be determined such as to achieve a median upper distance<br /> limit of approximately &#039;&#039;dref&#039;&#039; Angstrom for the peaks assigned to<br /> selected atoms in the &#039;&#039;peaklists&#039;&#039;. Only assignments to which a<br /> fraction of the total peak volume greater than the cutoff &#039;&#039;volcut&#039;&#039;<br /> is attributed are included when computing the median. This command<br /> sets the calibration constant of atoms, which may later be used to<br /> obtain upper distance limit restraints from assigned NOESY peaks by<br /> the command &#039;&#039;&#039;peaks calibrate&#039;&#039;&#039;.<br /> <br /> == See also ==<br /> <br /> * [[peaks calibrate]]<br /> * [[calibrate]]<br /> * [[caliba]]</div>

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