[phenixbb] Ligand building/refinement woes

Machius, Mischa Christian mischa_machius at med.unc.edu
Mon Jan 7 07:29:52 PST 2013

I seem to be having the hardest time building/refining NADPH (PDB code NAP).

When fetching this common ligand from within coot, Phenix (1.81-1168) subsequently does not seem to accept it and bombs noting all kinds of violations.

When I have Phenix automatically build NAP into the density, it does place NAP (albeit completely out of otherwise quite nice density). When I then take the coordinates, read them into coot together with the CIF that Phenix writes into the ligand_build directory, placing and refinement in coot works well, but subsequent refinement in Phenix, using the very same CIF, again bombs. Since hydrogens are often an issue when going from coot to Phenix I remove them before running Refine. I have also tried just refining the coordinates as they came out of ligand_build. But Phenix still bombs and doesn't seem to accept its own CIF.

I would have thought that a ligand as common as NAP wouldn't require a lot of gymnastics, perhaps not even reading CIF information, and that it would go all automatically.That's probably too optimistic on my part.

It's probably something silly, but I can't figure out what it is. 

Any ideas?

Many thanks in advance,

More information about the phenixbb mailing list