Hi all, thanks for posting on this topic.
In CryoSPARC v4.5.2, we have changed default parameters so that refinement jobs (including Homogeneous and Non-uniform Refinement) will not re-split particles by default, and will no longer raise an error (but instead issue a warning) if the two input half-sets are substantially different in size. Refinement jobs will still re-split if the input particles do not have any half-sets assigned (e.g., the particles are coming directly from 2D classification or Ab-initio reconstruction) or if the “Force re-do GS split” parameter is turned on.
The Particle Sets Tool job has also been updated to provide a mode where it can re-balance half-set splits in case they become unequal (by dropping particles from the larger half-set).
Repeated rounds of Reference Based Motion Correction and refinements will therefore now by default retain the particle split throughout a processing chain.
Thank you!