[phenixbb] Another dictionary question...

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Fri Aug 8 09:28:59 PDT 2008

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)?


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