[phenixbb] cis peptide question

Nathaniel Echols nechols at lbl.gov
Mon Jul 15 18:10:13 PDT 2013


On Mon, Jul 15, 2013 at 6:00 PM, Edward A. Berry <BerryE at upstate.edu> wrote:
> I have a cis-peptide in my structure. Phenix recognizes it
> and .geo file shows this is restrained to 0*:
>
> dihedral pdb=" CA  ALA A 401 "
>          pdb=" C   ALA A 401 "
>          pdb=" N   SER A 402 "
>          pdb=" CA  SER A 402 "
>     ideal   model   delta  harmonic     sigma   weight residual
>      0.00   -1.58    1.58     0      5.00e+00 4.00e-02 1.00e-01
>
> However in statistics printed with the output pdb, I have
> at least one dihedral that is flagged as off by about 180*:
>
> REMARK   3  DEVIATIONS FROM IDEAL VALUES.
> REMARK   3                 RMSD     MAX  COUNT
> REMARK   3   DIHEDRAL  : 12.902 168.987   3277
>                                 ^^^^^^^
> Could this be my cis peptide, or do I have a really bad dihedral somewhere
> else?

I would assume the latter, since the deviation of the cis-peptide is
only 1.58 degrees, but I think the .geo file should make this clear -
the dihedral angles will be sorted by residual (in descending order),
and these are coming from the same source as the statistics in the PDB
header.

-Nat


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