Hi @Joey,
Thanks for reporting the secondary issue about the Override Filtering BFactor parameter. For a brief explanation, the main use-case of these FSC filter and Sharpening override parameters (Override FSC Filtering and the parameters below it) is to enable apples-to-apples comparisons between two reconstructions. The normal filtering procedure in all Refinement and Reconstruction Only jobs involves: filtering the volume by applying the FSC calculated from the half-maps, and then sharpening with the estimated B-factor. Both of these steps depend on the reconstruction quality, which can make comparing two separate reconstructions difficult if you want to keep all of the filtering steps constant. The FSC filtering/sharpening override parameters allow one to bypass the FSC filtering step by manually specifying the lowpass filter resolution (Override Filtering Resolution), and the BFactor. However, these are really is only useful for developers who are carefully testing the effects of changing the reconstruction alignments – for most users in most cases, it makes sense to keep the filtering and sharpening behaviour as default.
Thus, the recommended way to independently test different sharpening B-factors is to run the Homogeneous Reconstruction Only job as normal, and then take the output unsharpened volume (map output) and run it through multiple Sharpening Tools jobs, each with different B-factors, as you have attempted. As @wtempel mentioned, newer versions of CryoSPARC allow a mask to be explicitly connected to the Sharpening Tools job. This fix was released in Patch 220518 on CryoSPARC v3.3.2, so updating to any version >= 3.3.2 + patch 220518 should allow for the desired behaviour.
Best,
Michael