Thanks - Ralph solved my problem. I looked in the cif dictionary and as I had originally added the NAG's using CNS the O1's were already removed. When I generated a dictionary using elbow, as the O1's were not present in the pdb coordinates, they did not get included in the dictionary - and hence the error. Not sure why it ran OK first time round... Simon On 8 Aug 2008, at 17:28, Ralf W. Grosse-Kunstleve wrote:
Hi Simon,
RuntimeError: delete_atom_in_place: unknown atom_id: O1
It is trying to delete the atom in the monomer library definition, as opposed to in the PDB file. It has to delete the atom in the monomer each time phenix.refine runs. So that looks OK. I'm guessing you somehow have the link twice. Could you look for a duplicate apply_cif_link block in your inputs? -- But I'm not sure that's it. If not, could you send me your inputs (directly, not to the list)?
Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb