Sorry to bother everyone.
I made some resources for showing some simple molecules (graphite, SF6,
etc) but since updating to Jmol 11.6 the molecules are showing with only
some of the covalent bonds.
The bonds are explicitly entered in the data file:
CONECT 199 200 200 (a double bond)
CONECT 2 3 13
If it's relevant: The data is stored as an inline variable, not a
separate file, and I use the jmolAppletInline() command.
Thanks for pondering this one!
That's pdb format, right?
I've done a quick test and it's working for me in both 11.4.6 and
Check the column positions of the atom numbers, might be that.
Not an explanation for your problem, but you could also dispose of
CONECT records and use Jmol "connect" command -- it's cleaner and
more flexible (partial bonds for example). And you can embed it in
the pdb file if you don't want to run a separate script.