Andrew, GRADE gives: ANP C5 C4 aromatic 1.388 0.011
ANP C5 C4 C3 126.8 0.7 i.e. essentially the same as Phenix, so I would go with that. The CCP4 values definitely could do with a re-examination: I've never heard of a "double bond" with a length of 1.49, and the angle looks like it's just been guessed! Cheers -- Ian On 15 September 2014 17:42, Andrew Leslie <and...@mrc-lmb.cam.ac.uk> wrote: > Dear Huw, > > Many thanks for this information. I had seen the notice about Molprobity > using CCTBX validation metrics, but I mistakenly thought that Phenix used > the CCP4 monomer library, which I think was true once but is clearly no > longer the case. > > Given the very small sigma values associated with the Phenix C4-C5 bond > length, it could be said to differ by 10.4 standard deviations from the > CCP4 monomer library value ! > > Many thanks to all others who have responded too. > > In response to Dale's comment, the frustrating thing is that this is not > interesting at all, it is merely confusing. The resolution of the new > structure is only ~3 Å, so there is no way that one can make meaningful > statements about distortions from standard geometry. The warnings merely > highlight the fact that we do not have adequate library entries. > > Best wishes, > > Andrew > > > > On 15 Sep 2014, at 17:14, Huw Jenkins <h.t.jenk...@me.com> wrote: > > > > > On 15 Sep 2014, at 15:24, Andrew Leslie <and...@mrc-lmb.cam.ac.uk> > wrote: > > > >> This would suggest that the standard dictionary that Molprobity uses > has changed, but I cannot find any reference to this on the Molprobity > pages. > >> > >> I would be very grateful if anyone can throw some light on this. > > > > MolProbity now uses the same target values as Phenix: > > > > "MolProbity4 structure validation now provides many of its validation > metrics through CCTBX, the open-source component of the Phenix > crystallographic package. CCTBX allows for consistent validation results > with Phenix, as well as added functionality, such as geometry > regularization of NQH flips” > > > > The target values for the C4-C5 bond length and the C5-C4-N3 bond angle > are quite different in the two libraries: > > > > > > ccp4-6.4.0/lib/data/monomers/a/ANP.cif > > > > ANP C4 C5 double 1.490 0.020 > > > > ANP C5 C4 N3 120.000 3.000 > > > > phenix-1.9-1692/chem_data/geostd/a/data_ANP.cif > > > > ANP C5 C4 aromatic 1.386 0.010 > > > > ANP N3 C4 C5 126.80 0.741 > > > > That explains the 8-10 sigma deviations reported by MolProbity but it > doesn’t explain which target values are (more) correct. > > > > > > > > Huw >
