Sorry for one more question: I am now trying to build in some sugar NAG residues that are N-linked to an Asn. I've used the parameter file below, and the first time phenx.refine ran perfectly. However after a bit of rebuilding I get the following error: result.delete_atom_in_place(mod_atom.atom_id) File "/usr/local/phenix-1.3-rc4/mmtbx/mmtbx/monomer_library/ cif_types.py", line 244, in delete_atom_in_place raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" % atom_id) RuntimeError: delete_atom_in_place: unknown atom_id: O1 I think this is referring to the O1 atom of the NAG sugar which the program had deleted the first time it ran in order to form the bond with the Asn. Is there any way of stopping phenix trying to delete this atom again? Thanks, Simon My cif_links.param file that is incorporated into my .def file second time round: refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 207 residue_selection_2 = chain A and resname ASN and resid 32