[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:

   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" %  
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?



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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