I am trying to convert http://crystallography.net/cod/2236556.cif to a file that I can open in Avogadro without some bonds disappearing. See this crystal structure is of tianeptine hydrochloride, yet many of the bonds are not shown when I open the CIF in Avogadro.
This is what the CIF is meant to be rendered like (shown in PyMOL):
while this is what I see in Avogadro (also displayed like this in Avogadro 2):
note how so many bonds are not shown properly. I suspect if I could convert the molecule to SDF or CML or some other 3D chemical format I'd be able to fix this issue and Avogadro will be able to render the file properly.
I have tried doing the file conversion with OpenBabel but the files generated look, when viewed in PyMOL or Jmol (which render the CIF fine), just like the CIF does in Avogadro with all the disconnected atoms.