[phenixbb] Hydrogens of ligands generated in elbow explode in coot realspace refinement

Schubert, Carsten [PRDUS] CSCHUBER at prdus.jnj.com
Thu Dec 6 12:58:23 PST 2007


when I refine a ligand with hydrogens in coot using realspace refinement, the hydrogens explode into the surrounding density. This only happens with ligand/cif files generated in elbow and not libcheck. Coot apparently needs and additional loop in the .cif file: _chem_comp_tree.xxxx, which is missing from the elbow output. 

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 ...

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

PS I am running the latest phenix (rc6) and coot 0.33 if that helps.


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