[phenixbb] cis peptide question

Pavel Afonine pafonine at lbl.gov
Mon Jul 15 23:27:00 PDT 2013

>>> 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.

Oh, makes it hard to resist to re-post this old link to slides #17-18 here:

The reason you could get away with this ok is because weights 
data/restraints used in phenix.refine are global.


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