Hi @LTP,
This is definitely an intended workflow for symmetry expansion. In general, symmetry expansion + local refinement (using any mask – could cover the whole dimer or just a monomer) can help whenever you are interested in seeing any features that would have been averaged together if symmetry was rigidly enforced. The only real “catch” with this workflow is that you should keep the GS half-set splits the same (i.e., make sure the “Force re-do GS split” parameter in local refinement off, which it should be by default). This ensures that all of the expanded copies of one particle stay in their same half-set, meaning you don’t have to worry about duplicate particles.
If you are seeing a quality improvement using local refinement with the mask covering the whole dimer, it’s possible that this is due to the finer angular search that local refinement does. I’ve sometimes seen FSC improvements on the order of 0.1 - 0.15 Å using symmetry expansion and local refinement (relative to just standard symmetric refinement) that I believe could be due to this – although this was with a relatively flexible helical filament. If you have non-uniform regularization & marginalization enabled, it’s likely also due to that.
Usually, if you are explicitly interested in resolving inter-subunit flexibility, you can try a mask covering just the monomer, but the success of this depends a lot on the align-ability of the monomer.
Best,
Michael