by the way, Jmol does not read the PDB
HYDBND The HYDBND records specify hydrogen bonds in the entry.
record.
Jmol just takes anything listed in the CONECT record as a hydrogen bond or salt
bridge to be an HBOND.
Bob
Jan wrote:
...
my opinion is, this is OK, hbonds should be created visible, as are
single or double bonds.
I agree.
There is some subtle interaction with some of the old
rasmol-compatibility
hbond code.
I will investigate.
This is a broader question but ...
Q: Is there ever a reason why someone would want hbonds turned off?
yes, normally they are not shown (simplify the image, less confusing
network), this can be done by
select NoHbondsPart
hbonds off
Q: Why should hbonds ever be treated differently from normal bonds?
these are weak interactions, but numerous
Q: If you read in a file that contains hbonds, do you want them displayed
by default?
yes, predefined hbonds should be seen on load pdb file.
Regards, Jan
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Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
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