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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