Found the problem! The hydrogen bond calculation was incorrectly
measuring the position
of the peptide amino hydrogen. This is fixed and testable at
http://www.stolaf.edu/people/hansonr/jmol/test/json/measure.htm
prototype jar files are at
http://www.stolaf.edu/people/hansonr/jmol/test/json
Now, in terms of calculating hydrogen bonds, all Jmol is doing is the
RasMol calculation (correctly now!), which simply generates intra-chain
hydrogen bonds specifically of the N-H...O=C type.
Miguel (I think) has experimented with other more general means of
calculation of hydrogen bonds; I could get interested in this, too. But
for now the RasMol variety is all that is operational. Is this something
people might be interested in working with us on? What would be more
difficult would be OH---O=C type hydrogen bonds, because the H is not
easily positionable.
Angel Herraez wrote:
I am playing with a beta-sheet model (part of 1A6Z.pdb) and have
found some incorrect behaviour:
"hbonds on" renders correct inter-chain H-bonds but also several
intra-chain H-bonds which, apart from striking, are too long (over 4
angstroms); this without counting the unlikely orientation of such
bonds.
As far a as I know, H-bonds are formed between atoms separated around
3 nm. Too long distances should never be rendered as H-bonds.
Apart from this, I also found that it the chain is interrumpted (by
removing in the PDB a portion of polypeptide between beta-strands),
no Hbonds are rendered between the now separated strands. There may
be a reason for this, but I'd rather prefer that H-bonds are
determined on the basis of geometry, not chains. There clearly may be
H-bonds among different subunits of a protein!
I am attaching the sample PDB file. Thanks for any advice
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