Hi Ewen

That's pdb format, right?

I've done a quick test and it's working for me in both 11.4.6 and 
11.6.16
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.
http://wiki.jmol.org/index.php/File_formats#Script_inline_within_a_mol
ecular_coordinates_file




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