I like using the intermediates mode with a window of 0 for 3D-VA display, to get sequential reconstructions from particles along the reaction coordinate of each mode. The only issue I find is that sometimes the first and last frame are a bit junky, presumably because these reconstructions don’t have many particles contributing to them.
I wonder if it might be worth having an option to split along the reaction coordinate in terms of equal particle bins (equal area), rather than just simply splitting by the reaction coordinate value? so effectively order by reaction coordinate value, and then generate reconstructions in bins of (for example) 20k particles.
This would also be useful when taking particle subsets for further refinement.