[phenixbb] riding hydrogen model
pafonine at lbl.gov
Wed May 27 06:04:13 PDT 2015
> I am currently refining a 1.75A structure and wanted to use the riding
> hydrogen model in pehnix.refine. From what I found in the manual and
> previous discussions on the mailing list and if I understand well,
> using riding Hs is advised for every resolution andthe way of doing
> this in phenix.refine is not Refmac-like but instead I should 1) put
> Hs using ReadySet, 2) select the ‘riding’ option for Hs and 3) use the
> PDB containing the H coordinates for deposition, even though they were
> not individually refined. In this case their contribution to
> scattering is also taken into account (which makes sense), which is a
> different way of treating riding Hs compared to Refmac, if I
> understand well.
I don't know how Refmac handles H so I cannot comment on this; the rest
I think is more or less accurate. Note, "riding" option is used by
default (unless it is neutron data).
Also, for some more details and illustration on how H contribute to
overall scattering and R-factors in different cases have a look at "On
contribution of hydrogen atoms to X-ray scattering" article here:
> Would it be possible to comment on this and in case I got things
> wrong, correct?
Perhaps one more thing we did not mention yet is that it's best to use H
towards the end when the model of the crystal structure is reasonably good.
> In fact for my structure, afteradding the Hs prior to refinement using
> ReadySet and using the riding option, I actually got Rfree dropping by
> 1% (from 19.5 to 18.5) and better clash score (~0.5 according to
This is well expected and in line with the illustrations in the article
I referred to above.
All the best,
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