Note, Molprobity has an option to use longer (neutron) X-H distances. Pavel
On Fri, Apr 28, 2017 at 11:46 AM, Tristan Croll <ti...@cam.ac.uk> wrote: > I believe the reason for the discrepancy here is that MolProbity by > default places the hydrogens according to the centroid of the electron > cloud (most relevant to x-ray crystallographic data) rather than the > nuclear position. In a polar bond like N-H the difference can be quite > substantial. > > Cheers, > > Tristan > > > > Tristan Croll > Research Fellow > Cambridge Institute for Medical Research > University of Cambridge CB2 0XY > > > > > On 28 Apr 2017, at 18:33, Bernhard Rupp <hofkristall...@gmail.com> wrote: > > Dear Fellows of the Bond, > > > > when validating a QM refined homology model with Molprobity, I noticed > various 8 sigma deviations in the carbon-hydrogen bond distances. > > Out of curiosity, I then used refmac to calculate riding Hs for the same > model, and at least in one instance (N-H backbone) there are > > significant differences between Molprobity and Refmac H bond distances > (differences to the QM distances in other > > instances I find interesting, but less relevant for us). > > > > The riding H vs Molprobity presumably should be consistent, because if we > use them in VDW restraints but > > they differ from the validation target, systematic bias will occur. I have > no feel how significant that effect > > might be – maybe someone more erudite can comment. > > > > Examples > > > > distance MP REF QM > > backbone N-H 0.86 1.01 1.00 > > phenyl C-H 0.93 0.93 1.09 > > > > Best, BR > > > > PS: If someone has accurate experimental values for CH distances I’d > appreciate a link. > > No access to CSD. > > > > ------------------------------------------------------ > > Bernhard Rupp > > Crystallographiae Vindicis Militum Ordo > > http://www.hofkristallamt.org/ > > b...@hofkristallamt.org > > +1 925 209 7429 <(925)%20209-7429> > > +43 767 571 0536 <+43%207675%20710536> > > ------------------------------------------------------ > > Many plausible ideas vanish > > at the presence of thought > > ------------------------------------------------------ > > > >
