Dear community,
I am probably disturbing a sleeping bear, but I'll post anyways...
Reading the thread on hydrogen deposition with the model, I came accross
several arguments that make sense on their own, but when put together are
puzzling and dont seem to converge to an answer. (I do realize however, there
probably isnt "an" answer...)
-Some argued that depositing riding hydrogens with the model may imply that
your data had enough information for you to include hydrogen atoms in the final
model. This is definetely a problem especially when dealing with
non-experienced users that may think the model is more accurate than it really
is.
-It seemed to be consensus, that when softwares use hydrogen restraints it can
be beneficial geometrically and also can make your model a better description
of your x-ray data. I have seen in a particular software that optmizing
hydrogen atom scattering can improve Rfree by as much 1.5% in a high resolution
structure.
Based on these two main arguments, many would agree that hydrogens should be
included throughout refinement but not deposited.
So this brings me to last point that was also mentioned in the old thread. 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?
So how would one avoid this Catch-22?
