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?
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.