[phenixbb] Riding H

Nathaniel Echols nechols at lbl.gov
Fri Oct 29 15:35:51 PDT 2010

On Fri, Oct 29, 2010 at 2:56 PM, Jianghai Zhu <jzhu at idi.harvard.edu> wrote:
> 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.


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