Dear @simonbrown,
As of v3.0+, you can re-center particles upon extraction by passing them back through an extract from micrographs job. Re-centering will be done by default if the particles have been previously aligned to 2D or 3D references (there is a parameter called “Recenter using aligned shift” that is active by default). This will use the shifts determined by any 3D reconstruction/refinement, or if not present, from 2D classification. Note that there isn’t yet an option to manually set the desired center location to some arbitrary location on the 3D or 2D reference.
Best,
Michael