Dear phenix community

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 and the 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.

Would it be possible to comment on this and in case I got things wrong, correct?

In fact for my structure, after adding 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).