https://cyana.org/w/index.php?action=history&feed=atom&title=CYANA_Commands%3A_atoms_glomsa 2026-04-20T02:24:04Z Revision history for this page on the wiki MediaWiki 1.45.1 https://cyana.org/w/index.php?title=CYANA_Commands:_atoms_glomsa&diff=4482&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 /> ; cutoff=&#039;&#039;real&#039;&#039;: (default: 0.4)<br /> ; threshold=&#039;&#039;real&#039;&#039;: (default: 0.4)<br /> ; fr <br /> ; single <br /> <br /> == Description ==<br /> <br /> The &#039;&#039;&#039;atoms glomsa&#039;&#039;&#039; command searches for stereospecific assignments of<br /> diastereotopic atoms matched by the selection &#039;&#039;string&#039;&#039; by analyzing<br /> the distances that are restrained by an upper distance limit in the<br /> selected conformers. The command provides the functionality of the<br /> former separate program GLOMSA (&quot;GLObal Method for Stereospecific<br /> Assignments&quot;). By default, the selection made in the most recent &#039;&#039;&#039;atoms<br /> select&#039;&#039;&#039; command is used, or all diastereotopic atoms if no selection<br /> has been made so far. Stereospecific assignment proposals are reported<br /> for those diastereotopic pairs for which the difference between the<br /> upper bounds from the two diastereotopic atoms to a third atom exceeds<br /> the &#039;&#039;cutoff&#039;&#039;, given in Angstrom, and the corresponding average distance<br /> difference in the selected conformers is larger than the &#039;&#039;threshold&#039;&#039;,<br /> also given in Angstrom, in at least the chosen &#039;&#039;fraction&#039;&#039;, given in<br /> percent, of the selected conformers. Single distance restraints from<br /> one but not the other of two diastereotopic partners to a third atom<br /> can be considered by setting the option &#039;&#039;&#039;single&#039;&#039;&#039;. The &#039;&#039;&#039;atoms glomsa&#039;&#039;&#039;<br /> command reports proposals for stereospecific assignments but does<br /> not fix the stereospecific assignment as the &#039;&#039;&#039;atoms stereo&#039;&#039;&#039; command.<br /> <br /> Further reading:<br /> <br /> * Guntert et al. J. Mol. Biol. 217, 517-530 (1991).<br /> * Guntert et al. J. Mol. Biol. 217, 531-540 (1991).<br /> <br /> == See also ==<br /> <br /> * [[atoms stereo]]<br /> * [[stereoassign]]<br /> * [[habas]]</div>

Admin