Yuri, scattering from H is always included when input PDB file has H atoms in it (and it is a refinable parameter), regardless whether you use "hydrogens.refine=individual" or "hydrogens.refine=riding". The only (main) difference between the two options is that "riding" option does not add extra individual refinable parameters arising from H atoms. Again, more details are here and in references therein: "On contribution of hydrogen atoms to X-ray scattering" http://phenix-online.org/newsletter/ The bug I mentioned in my reply is that when "hydrogens.refine=riding" is used the scattering from H is included everywhere but maps, so that was explaining to me why you still see H atoms in residual map even though you have them in your model. I will fix this bug as soon as I can, but probably not in a next few days. Now you are saying that you tried both options and that did not make any difference map-wise. This is something I can't explain. Therefore, could you please send me the model and data, and I will investigate what's going on. Thanks, Pavel On 3/1/12 6:57 PM, Yuri wrote:
Sue: I am not sure they are being included... I have the option checked, but the R values and difference maps tell me otherwise Pavel: A bug? That would be consistent with the behavior I observe. Even when I enable refinement with hydrogens individual or riding, i see essentially no difference in maps or Rfree values.