[phenixbb] peptide link

Nigel Moriarty nwmoriarty at lbl.gov
Thu Nov 10 11:39:58 PST 2011


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


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.


On Thu, Nov 10, 2011 at 11:21 AM, Christian Roth
<christian.roth at bbz.uni-leipzig.de> 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
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

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