Hi Oli,
I should clarify what I meant by “it doesn’t actually produce a transformation of the original volume.” Homogeneous Reconstruction Only does successfully produce a very similar volume in the intended new location, but it is not actually a transformed copy of the original volume generated by the non-uniform refinement. Instead it is a transformed copy of the volume that would have resulted if I’d run Homogeneous Reconstruction Only on the original output of my non-uniform refinement job—and I think this is due to the mentioned difference(s?) between the way non-uniform refinement and homogeneous reconstruction generate maps. The very slight differences would not matter if the particle poses were what I was after (as in the Align 3D → local refinement pipeline that you mentioned), but in this case I’m after the volume itself (for things like model building and deposition). Does that make sense?
By the way, what I’m actually working on is taking the result of a local refinement (with non-uniform refinement on) on a subvolume that I previously moved to the center of the box and moving it back out to the position where it sat in the original consensus reconstruction. The reason I put it in the center of the box in the first place was your comment from several years ago here (Manual definition of refinement alignment center - #6 by olibclarke). Is it still your preferred workflow to move messy peripheral domains to the center of the box for local refinement?