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On 9/15/2014 9:42 AM, Andrew Leslie 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. > Which is interesting. ;-) To be serious, I do think this is interesting. Apparently someone looking at this molecule has decided that this bond should be 1.49 A with a sigma of 0.02 A while someone else looking at the same molecule concluded it should be 1.386 A with sigma 0.01 A. The most significant source of uncertainty in this target value (whether it is a double bond or an aromatic bond) has been ignored. Each library is constructed ignoring the possibility of error in categorizing the type of bond. I think the lesson is that the sigmas are being seriously under estimated when the target values are not derived from real high resolution structures. Isn't it also interesting that the double bond of ccp4 is longer than the aromatic bond of phenix? Not what I would have expected. Dale > 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 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.22 (MingW32) iEYEARECAAYFAlQXHHMACgkQU5C0gGfAG11EwgCbBss46rjpxSgZd6g5RghahFbF t58AniRhSFrNZxdu5y4DZPCVZC3RCJbZ =ngD/ -----END PGP SIGNATURE-----
