On Fri, Oct 29, 2010 at 2:56 PM, Jianghai Zhu
That is what I thought. But wouldn't the nuclear distance be more accurate? and we should use the molprobity bond length, the longer one?
I'm not sure what is most accurate from the standpoint of a molecular modeler or chemist, but as far as X-ray diffraction is concerned, the shorter distance is better - however, the difference in R-factors is minimal, even at atomic resolution. Internally, we're using the same monomer library that Refmac uses, so it's non-trivial to switch to the longer distances. I suspect it might improve the geometry, but I haven't tested this. For what it's worth, the validation tools in PHENIX (which includes most of Molprobity at this point) always strip and re-add hydrogens before calculating clashes, so the result will always reflect the longer bonds. -Nat