Christian SNN is a VERY non-standard peptide. By that I mean that the atom names do not include C, CA, O, N which phenix.refine uses to automatically link a non-standard residue into the chain. This is also why you attempts to link it using the standard TRANS linking which needs a C and N in the residues. The best thing to do is create a cif_link http://www.phenix-online.org/documentation/refinement.htm#anch82 which I can help with if you send me the DPB directly or at least the three residues in question. phenix.link_edits should have worked also but is not as accurate as the above but I'd like to debug that also. Nigel On Thu, Nov 10, 2011 at 11:21 AM, Christian Roth wrote:

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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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