[phenixbb] Another dictionary question...
Simon Kolstoe
s.kolstoe at ucl.ac.uk
Fri Aug 8 06:46:20 PDT 2008
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
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