On Saturday, 12 May 2012, Yuri Pompeu wrote: > If you used riding hydrogens throughout refinement and arrived at a final > model that you believe best describes your x-ray data to a certain level of > accuracy (Rvalues, geometry, map CC, etc...) would you not be invalidating > the whole refinement process by going in and removing the hydrogen atoms > right before deposition?
My view: You are not "removing hydrogen atoms" at all. You are stating that the model being deposited includes riding hydrodens. The consumer of your model can regenerate the individual hydrogen coordinates from that information if needed, just as refmac does when you start a new refinement cycle with the riding hydrogen model selected. You don't need to output the individual hydrogen coordinates between cycles, or at deposition time, because they are adequately described by the riding hydrogen model. You might as well ask "why do we remove all copies of the molecules in the crystal except for those in a single asymmetric unit?" They are not really "removed"; they are implicit in the statement of the crystallographic symmetry. Ethan