Good news! Jmol 12.0 will be able to calculate hydrogen bonds for any model.
All you do is to indicate in the CALCULATE command two atom sets.
calculate HBONDS {*} {*}
will do it.
When hydrogen atoms are present, this is the sort of bond you would expect.
You can limit the type of atoms to which the hydrogen bonds are formed by
changing the second set:
calculate HBONDS {*} {nitrogen}
When hydrogen atoms are not present, as for typical PDB files, the bonds are
drawn between O-N and N-N connections as well as O-O connections that are
not both carbonyl carbons.
See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=118
--
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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