That's it. The logic is this:
If you ask for
calculate hbonds
now that Jmol has "real" hydrogen-bond calculation capability, for all
models, not just PDB files, Jmol will calculate hbonds for traditional PDB
files (not containing hydrogen atoms) just as before, but if hydrogen atoms
are included in the selected atom set, Jmol assumes you want actual hydrogen
bonds, not "pseudo" hydrogen bonds between N and O atoms of a protein or
nucleic acid.
You are right, though, that it is a change in the default behavior. Your
solution is correct -- first
select not hydrogen
then do the calculation if you want the pseudo-hydrogen-bond type you are
used to seeing.
Bob
2010/12/13 Angel Herráez <angel.herr...@uah.es>
> After looking at the online doc I have found, quite by chance, a hint
> for the change in behaviour.
>
> The file in question has 2 hydrogen atoms (added manually since that
> is a non-H pdb file). Other 2 files that I use (single nucleotide
> pairs) have a full set of hydrogens.
> On any on them,
> hbonds calculate
> calculate hbonds
> both fail to produce any bonds in Jmol 12.
>
> If I do
> select not _H
> before, then the bonds are generated. That's the way it's written in
> the doc, but I find no sense in it.
>
> I gather this is something new in relation to new and better ways of
> calculating H bonds in Jmol 12, but still don't see the convenience
> of this behaviour -- and in fact I think it will break many existing
> scripts.
> What is the expected behaviour for a H-containing model when one uses
> calculate hbonds? Would it do anything under any circumstances?
>
>
>
>
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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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