Hi @miwoodso, my apologies for not figuring this out sooner. When working with shifted particles, Recenter using aligned shifts during Downsample Particles will undo the shift you applied in the particle’s location field. So they will still look shifted in a reconstruction, but their locations on the micrograph will return to the particle center.
If you turn this parameter off (the default for Downsample Particles) the shifts are preserved.
