Schubert, Carsten [PRDUS] wrote:

when I refine a ligand with hydrogens in coot using realspace refinement, the hydrogens explode into the surrounding density.

This is a known issue with Coot.

This only happens with ligand/cif files generated in elbow and not libcheck.

Coot has had some tuning vs libcheck, but little vs elbow.

Coot apparently needs and additional loop in the .cif file: _chem_comp_tree.xxxx, which is missing from the elbow output.

Hmm... I wonder why you think so. This may well be addressed in a more modern Coot.

Unfortunately the geometry generated by libcheck is pretty dismal, so I can probably get around this by running libcheck on the refined coords from elbow ...

Urgh - non-optimal.

Nigel, is it possible to fix elbow for the next rc?

I'm not sure that it is on Nigel's door that you should be banging. Maybe you, me and Nigel can get this sorted out (preferably testing with something non-proprietary).

coot 0.33

0.4 will be out soon. I'd recommend the upgrade. HTH, Paul.