[phenixbb] Scattering from riding hydrogens?

Tim Fenn tim.fenn at gmail.com
Tue Nov 15 17:25:14 PST 2011

Sorry I'm chiming in a bit late here, but I think its worthwhile to point
out that hydrogen atoms are highly influenced by (and affect!) prior
chemical forces - primarily electrostatics/polarization and van der Waals.
 Given the difficulty in refining hydrogen atoms against the scattering
data alone, I would argue a rigorous model for electrostatics/vdw terms in
the prior is essential.  This also makes it a moot point of having to
decide how to refine hydrogen atoms and dealing with tricky cases (like
rotatable degrees of freedom or water molecules).  There is technology
available to do this already and some publications on its importance in the
refinement process, for those that are interested.


On Mon, Nov 14, 2011 at 6:27 PM, Pavel Afonine <pafonine at lbl.gov> wrote:

> **
> Hi Damian,
>  This question was motivated by discussions of whether or not to deposit riding hydrogens in the PDB,
> this was discussed so many times on both ccp4bb and phenixbb... So, very
> briefly, I do not know any single reason (and can't even imagine one) why
> one may want to remove hydrogens before PDB deposition. Most of reasons why
> hydrogen atoms should not be removed are listed in:
> phenix.model_vs_data: a high-level tool for the calculation of
> crystallographic model and data statistics. P.V. Afonine, R.W.
> Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W. Moriarty, J.S. Richardson,
> D.C. Richardson, A. Urzhumtsev, P.H. Zwart, P.D. Adams J. Appl. Cryst. 43,
> 677-685 (2010).
> and lots of hints here:
> Joint X-ray and neutron refinement with phenix.refine. P.V. Afonine, M.
> Mustyakimov, R.W. Grosse-Kunstleve, N.W. Moriarty, P. Langan, and P.D.
> Adams Acta Cryst. D66, 1153-1163 (2010).
>  So in the context of Phenix and Fcalc, do the positions of the riding hydrogens matter?
> Yes, positions matter. As well as B-factors and occupancies. Note,
> B-factors of H are inherited from parent atoms with some multiplier that
> ranges from 1 to 1.5 (see SHELXL manual for details).
>  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?
> No, if there are no H atoms in input PDB file, phenix.refine will not try
> to account for missing H in any way.
> Pavel
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