[phenixbb] peptide link

[Christian Roth]

Hi,

I have an modified aminoacid in my peptide chain (backbone modified). I have a 
cif file and I refined it previously in Refmac. I put the Link  definition in the 
pdb and Refmac has interpreted the peptide link as  I wanted. Now I did a run 
in phenix to compare  the results and the chain is broken I created the SNN 
cif file with ReadySet Reel and I tried to incorporate the link definition via 
GUI in the following way
 apply_cif_link:
    data_link: TRANS
    residue_selection_1: chain A and resseq 366
    residue_selection_2: chain A and resseq 367
  apply_cif_link:
    data_link: TRANS
    residue_selection_1: chain A and resseq 367
    residue_selection_2: chain A and resseq 368
Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 7983
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 496, 7926
          Unusual residues: {'SNN': 1}
          Classifications: {'undetermined': 1, 'peptide': 495}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 37, 'TRANS': 456, None: 2}
            Not linked:
              pdbres="ASP A 366 "
              pdbres="SNN A 367 "
            Not linked:
              pdbres="SNN A 367 "
              pdbres="GLY A 368 "
          Chain breaks: 1
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
This fails with an error message that it cannot interpret the links. In my 
previous pdbs I have also defined the atoms which I wanted to link. Maybe I 
have to do this also somhow in Phenix. 
I have tried to extract the Link definition using phenix.link_edits but the 
resulting .edits file is empty. 
How can I resolve issue?

Thanks

Christian