[phenixbb] cis peptide question

Edward A. Berry BerryE at upstate.edu
Mon Jul 15 21:44:42 PDT 2013

Nathaniel Echols wrote:
> On Mon, Jul 15, 2013 at 6:00 PM, Edward A. Berry <BerryE at upstate.edu> wrote:
>> 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

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