Bob Hanson wrote:
by the way, Jmol does not read the PDB
HYDBND The HYDBND records specify hydrogen bonds in the entry.
record.
that is, what I call predefined hbond, all in-file-bonds should show up
on load
HYDBND Identification of hydrogen bonds. (supplements CONECT
| REMARK2?0)
SLTBRG Identification of salt bridges (supplements CONECT,
REMARK290)
LINK Identification of inter-residue bonds. (supplements
CONECT | REMARK290)
SSBOND Identification of disulfide bonds. (CONECT generated
if both cysteine SG are present else REMARK290)
I think it is a good idea to make (non-covalent) bond calculation
separable from author-defined bonds.
Jmol just takes anything listed in the CONECT record as a hydrogen
bond or salt bridge to be an HBOND.
it looks like Jmol 10.00.52 does backbone hbond-calculation and show up
on-load, I would prefer if only the CONECT HYDBNDs are visible after
file-load, that I was pointed to the authors intention to highlight just
this HYDBND
...
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.
the CONECT HYDBNDs,
calculated and added hbonds should show up as they are inserted by the
users script.
I just checked in code which changes hbond behavior. hbonds are now
created with the default bond radius rather than with a default radius of
0.
I'm against hbonds calculation and show up on load pdb file.
There is a problem separating hbond calculation and hbond-display in
RasMolScript, for maximal compatibility
hbond
hbond on
# may start calculation if needed and set default hbond visibility style
connect auto hbond (selected) (selected)
# (within the current selection)
hbond <number>
# may define a display style without starting any calculation.
Regards, Jan
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