Hi @lizellelubbe,
This is an interesting post! One potential factor contributing to the discrepancy could be the number of particles in each stack. Since extraction filters out particles that (upon extraction) will exceed the edge of the micrograph, larger box sizes will result in less particles extracted, although you likely have considered this already. In any case, what is the difference in the number of particles in the large vs small box size stacks?
Other than that, there’s a fair number of internal parameter choices that are dependent on the box size, and it’s possible that one of those could also be contributing to the resolution discrepancy. For example, the final precision (i.e. step size) in particle alignment shifts is technically proportional to the box size: for a larger box size, shifts are sampled more coarsely (although, this was tuned to go well beyond the alignment resolution needed for most datasets). Also, the initial iterations of branch-and-bound alignment start at a constant radius in Fourier space, which was also tuned on a large number of real datasets, and it’s possible that the tuning wasn’t aimed at very large box sizes relative to the particle size.
Your point on there being more noise in the Fourier domain also definitely makes sense, and could also definitely be a cause. I think practically it makes sense to go ahead and use the smaller box size result, as long as CTF aliasing is not an issue at the box size you’ve chosen (This is a useful utility from the RELION developers to visualize what the CTF looks like with your parameters).
Best,
Michael