[phenixbb] peptide link
Nigel Moriarty
nwmoriarty at lbl.gov
Thu Nov 10 11:39:58 PST 2011
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
<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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
--
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
More information about the phenixbb
mailing list