[phenixbb] Scattering from riding hydrogens?

Nathaniel Echols nechols at lbl.gov
Mon Nov 14 16:33:58 PST 2011

On Mon, Nov 14, 2011 at 4:12 PM, Damian Ekiert <dcekiert at scripps.edu> wrote:
> As I understand things, the positions of the riding hydrogens (from an input PDB file) would would be incorporated into the calculation of Fcalc (I guess automatically now and before when contribute_to_f_calc = True).  If this is correct, then removing riding hydrogens before deposition seems very problematic, as they were effectively used in the calculation of R/R-free, etc.  However, if the contribution of hydrogens is more abstract (e.g., the riding hydrogens are not used in the calculation, but the presence of hydrogens in the protein in the crystal are accounted for in some other way), leaving them out of the deposition is somewhat less of a problem (setting aside for a moment any other reason for depositing them, such as the difficulties in re-hydrogenating the protein later on, etc.).

For what it's worth, I've been doing a lot of data mining of new
structures in the PDB recently, and the recalculated R-factors for
high-resolution structures (including those originally refined with
PHENIX) are typically 1-2% higher than reported.  So stripping the
hydrogens really is leaving out a non-trivial component of the model.
(I don't see very much change at low resolution.)

> So in the context of Phenix and Fcalc, do the positions of the riding hydrogens matter?  And if they don't, does this mean that when an input model has zero hydrogens, Phenix is still trying in some way to account for the unmodeled/invisible hydrogens that we know are in there?

I think the answer to the first question is "sort of" (moreso for
neutron than X-ray diffraction), but the answer to the second part is
that it does account for them in the geometry restraints (by inflating
atomic radii for the nonbonded interactions - the chirality restraints
also compensate), but not in the scattering.  (The scaling of F(calc)
and F(obs) usually takes care of any resulting difference in R-factors
at medium-to-low resolution, but I don't know how this changes the
optimization target.)


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