[phenixbb] riding hydrogen model

Filip Qbukarski filip_qbukarski at yahoo.com
Tue May 26 11:42:45 PDT 2015

Dear phenix community 

I am currently refining a 1.75A structure and wanted to usethe riding hydrogen model in pehnix.refine. From what I found in the manual andprevious discussions on the mailing list and if I understand well, using ridingHs is advised for every resolution and the way of doing this in phenix.refine is notRefmac-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 fordeposition, even though they were not individually refined. In this case theircontribution to scattering is also taken into account (which makes sense),which is a different way of treating riding Hs compared to Refmac, if Iunderstand well. 

Would it be possible to comment on this and in case I got thingswrong, correct?In fact for my structure, after adding the Hs prior to refinement using ReadySet and using theriding option, I actually got Rfree dropping by 1% (from 19.5 to 18.5) and better clash score (~0.5 according to Molprobity).

Thanks in advancebestFilip
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