Re: [phenixbb] cis peptide question

Nathaniel Echols wrote:

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

...

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.

Thanks, got it- its a ligand. The cif file fdoesn't allow a 2-fold rotation that it should. "sinusoidal 1" should be "sinusoidal 2", I guess. or change 90 to -90 for this structure? Interestingly the incorrect restraint doesn't keep it from fitting the density beautifully.