Eric, see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=118
Should do the job -- also calculates hydrogen bonds for standard models that
DO have H atoms.
Bob
On Mon, Mar 29, 2010 at 10:23 PM, Eric Martz <[email protected]>wrote:
> Currently, FirstGlance in Jmol suggests hydrogen bonds whenever a
> nitrogen or oxygen is within 3.5 Angstroms of another nitrogen or
> oxygen. This crude method fails to take into account whether or not
> either atom actually has a hydrogen to donate, and the angle of the
> acceptor to the donor.
>
> If the model contains all hydrogens (or once Jmol can add them), is
> Jmol capable of selecting donor-acceptor pairs using not only
> distance, but angular criteria?
>
> For example, in 3hyd,
>
> see http://proteopedia.org/wiki/index.php/User:Eric_Martz/Sandbox_10
>
> [Leu1]:A.N #1 is donating [Leu1]:A.H3 #11 to HOH8 #135 at 126.4
> degrees (donor to acceptor distance 2.8 Angstroms), or to HOH10 #137
> at 154.9 degrees (D-A distance 3.1 A).
>
> Can I select one or the other (and which would be the stronger
> hbond?) based on these angles? What would the script commands be?
>
> Thanks, -Eric
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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