Thanks, this was a very satisfying find.
Why the difference: Jmol code is running through "polymers" not "chains",
and I think the breaks define distinct polymers.
Another difference is the minimum hydrogen bonding distance,
which is 0.7 Angstroms in Jmol but 0.5 Angstroms in RasMol.
I can't ima
Great work, Bob!
I am not clear as to what happens with inter-chain bonds. Are they
not being calculated? And in my example, they weren't even inter-
chain, the chain was interrupted but was the same "A" chain. Rasmol
gives Hbonds irrespective of the chain cut.
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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
I've checked in a fix for this. It involved adding a check for maximum
distance; seems odd that this was not there before. Miguel: comment?
Hydrogens are calculated based on geometry, but only within chains.
Prototype test is at
http://www.stolaf.edu/people/hansonr/jmol/test/json/measure.htm
OK, I see them. Yes, this is wrong. I'll look into it.
Hydrogen bonds are only about 1.8 - 2.0 Angstroms, but because the H
atom itself is not shown, the distance between the two heteroatoms
should be about 2.6-3.1 Angstroms.
Someone can probably summarize how hydrogen bonds are determined in
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