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Distances hbond - Revision history
2026-04-20T02:22:10Z
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https://cyana.org/w/index.php?title=Distances_hbond&diff=3717&oldid=prev
Admin: 1 revision
2009-01-28T18:18:39Z
<p>1 revision</p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:18, 28 January 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Parameters ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Parameters ==</div></td></tr>
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https://cyana.org/w/index.php?title=Distances_hbond&diff=2915&oldid=prev
Admin: 1 revision
2009-01-28T18:12:27Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 20:12, 28 January 2009</td>
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https://cyana.org/w/index.php?title=Distances_hbond&diff=2103&oldid=prev
Admin: 1 revision
2009-01-28T17:25:56Z
<p>1 revision</p>
<p><b>New page</b></p><div><br />
== Parameters ==<br />
<br />
; donors=''string'': (default: *)<br />
; acceptors=''string'': (default: *)<br />
; distance=''real'': (default: 3.5)<br />
; angledonor=''real'': (default: 90.0)<br />
; angleacceptor=''real'': (default: 75.0)<br />
; structures=''integer'': (default: ''none'')<br />
; weight=''real'': (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 '''donors''' atom selection and other atoms that match the<br />
'''acceptors''' atom selection. Only atoms that are declared as potential<br />
hydrogen donors or acceptors in the '''ATOMTYPES''' 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 '''structures'''<br />
parameter:<br />
<br />
* The distance between the donor hydrogen and the acceptor must be<br />
shorter than the cutoff given by the '''distance''' parameter (in Angstrom).<br />
* The angle at the donor hydrogen must be larger than the cutoff given<br />
by the '''angledonor''' parameter (in degrees).<br />
* The angle(s) at the acceptor must be larger than the cutoff given<br />
by the '''angleacceptor''' 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 '''ambiguous'''<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 '''weight'''parameter. By default, unless the '''append'''<br />
option is set, these distance restraints replace all existing distance<br />
restraints.</div>
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