Hello,
The requirement sounds extremely suspect: every atom in the structure
contributes to every reflection, so refining "only some atoms" makes as
little mathematical sense as refining against "only a subset of
reflections".
I agree with you that the requirement sounds dubious.
But the specific argument you make is not quite right.
Two common counter-examples are real-space refinement and rigid-body
placement of a known fragment relative to an existing partial model.
Not so: they're tricks to get out of local minima and maybe improve
phases, but they're /not/ useful for generating the model that "best"
fits the data,
I completely agree with Ethan. Although the overall goal of refining
B-factors only for a subset of atoms is not clear (there are at least
three example where I do it in phenix.refine - I won't go into
technicalities here, it's hidden under the hood and no-one knows -:) ),
doing so makes perfect sense in general.
Or would one deposit a model for which real-space refinement has been
the final step?
Of course you would. Refinement - in whatever space - is just a
trick/blackbox to get your model to correspond to the data, and how you
do it: in real, reciprocal or both spaces, manually moving atoms or
letting minimizer or grid search do that - it does not matter.
Pavel.
