[phenixbb] riding hydrogen model

Pavel Afonine pafonine at lbl.gov
Wed May 27 06:04:13 PDT 2015

Hi Filip,

> 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 
> Molprobity).

This is well expected and in line with the illustrations in the article 
I referred to above.

All the best,
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