[phenixbb] cis peptide question
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
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
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