On Mon, Jul 15, 2013 at 6:00 PM, Edward A. Berry
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