This feature is now running on V3.1, so I was wondering what happens to particles coordinates that are moved outside the volume and is there a way to remove them. I did local refinement on a domain and then centered that portion and did symmetrized local refinement and got similar results before and after centering the domain, but when doing Homogenous Refinement (without symmstry), the structure deteriorated greatly even compared to the original structure taken prior to any localized refinement. I am thinking this is because part of our structure has left the box (we are working on protein lattice) and the particle alignments are no longer valid/useful.
Is there a way to drop these particles? I was hoping Class Probability Filter would be able to recognize particles with alignments outside the box, but even after homogenous reconstruction the alignment scores seem to not me affected by the shift.
The structure extended beyond our box size normally, so we are used to working with mask truncated structures.
Thank you