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
