https://cyana.org/w/index.php?action=history&feed=atom&title=CYANA_Commands%3A_distances_hbond 2026-04-20T02:24:13Z Revision history for this page on the wiki MediaWiki 1.45.1 https://cyana.org/w/index.php?title=CYANA_Commands:_distances_hbond&diff=4526&oldid=prev 2009-01-28T23:35:41Z

<p>1 revision</p> <p><b>New page</b></p><div><br /> == Parameters ==<br /> <br /> ; donors=&#039;&#039;string&#039;&#039;: (default: *)<br /> ; acceptors=&#039;&#039;string&#039;&#039;: (default: *)<br /> ; distance=&#039;&#039;real&#039;&#039;: (default: 3.5)<br /> ; angledonor=&#039;&#039;real&#039;&#039;: (default: 90.0)<br /> ; angleacceptor=&#039;&#039;real&#039;&#039;: (default: 75.0)<br /> ; structures=&#039;&#039;integer&#039;&#039;: (default: &#039;&#039;none&#039;&#039;)<br /> ; weight=&#039;&#039;real&#039;&#039;: (default: 1.0)<br /> ; ambiguous <br /> ; append <br /> <br /> == Description ==<br /> <br /> This command analyzes the selected structures with respect to potential<br /> hydrogen bonds and generates upper and lower distance bounds to<br /> restrain potential hydrogen bonds.<br /> <br /> Potential hydrogen bonds are searched between hydrogen atoms that<br /> match the &#039;&#039;&#039;donors&#039;&#039;&#039; atom selection and other atoms that match the<br /> &#039;&#039;&#039;acceptors&#039;&#039;&#039; atom selection. Only atoms that are declared as potential<br /> hydrogen donors or acceptors in the &#039;&#039;&#039;ATOMTYPES&#039;&#039;&#039; entry of the residue<br /> library are taken into consideration.<br /> <br /> A potential hydrogen bond must fulfill the three following criteria<br /> in at least as many selected structures as defined by the &#039;&#039;&#039;structures&#039;&#039;&#039;<br /> parameter:<br /> <br /> * The distance between the donor hydrogen and the acceptor must be<br /> shorter than the cutoff given by the &#039;&#039;&#039;distance&#039;&#039;&#039; parameter (in Angstrom).<br /> * The angle at the donor hydrogen must be larger than the cutoff given<br /> by the &#039;&#039;&#039;angledonor&#039;&#039;&#039; parameter (in degrees).<br /> * The angle(s) at the acceptor must be larger than the cutoff given<br /> by the &#039;&#039;&#039;angleacceptor&#039;&#039;&#039; parameter (in degrees).<br /> <br /> Unambiguous hydrogen bond restraints are generated, if a donor hydrogen<br /> is involved in a single potential hydrogen bond. If several potential<br /> hydrogen bonds can be found for a donor hydrogen, then ambiguous<br /> hydrogen bond restraints are generated only if the &#039;&#039;&#039;ambiguous&#039;&#039;&#039;<br /> optionm is set.<br /> <br /> The restraints consist of (unambiguous or ambiguous) upper distance<br /> limits of 2.0 Angstrom between the donor hydrogen and the acceptor<br /> atom and of 3.0 Angstrom between the acceptor atom and the atom that<br /> is covalently bound to the donor hydrogen. Unambiguous lower distance<br /> limits of 1.8 and 2.7 Angstrom, respectively, are generated for the<br /> same distances. The relative weight of these distance restraints can<br /> be set with the &#039;&#039;&#039;weight&#039;&#039;&#039;parameter. By default, unless the &#039;&#039;&#039;append&#039;&#039;&#039;<br /> option is set, these distance restraints replace all existing distance<br /> restraints.</div>

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