When particles are small, embedded in micelles, contaminated, or flexible, auto-masking tends to be far too optimistic, leading to hopeless over-refinement. I wish we could select “loose” or spherical mask FSC to decide on what resolution to use in the next refinement cycle in homogenous or NU refinement jobs. Would it be possible to add such a setting? This will help to compare particle subsets without re-running the jobs with a range of “maximum align resolution” parameter.
Also, there used to be a setting (which IIRC never really worked) to fix a B factor for sharpening at each iteration. I think it would be useful, because very often the resulting maps are over-sharpened. A separate sharpening job is an easy one, but the projects quickly get very messy. Again, I am looking for a quick way of comparing subsets of particles.