I generally run cryosparc refine, then relion_reconstruct w/ same symmetry, postprocess, then polish. I am wondering why relion_reconstruct half maps give different final resolution (~0.11A worse) than the cryosparc half maps when using the same mask.
@user123 I had recently posted a similar question and got some helpful answers from @olibclarke thread: Cryosparc FSC resolution vs Relion FSC resolution
I would definitely love to know more about what all the different FSC curves (and resolutions) that cryosparc generates, mean…
I think this discrepancy has more to do with how relion_reconstruct generates the half maps, rather than the resolution calculation (I am using the same masks). I recall a popular post/discussion on how cryosparc calculates the fsc with various masks. This may be it, but I can’t recall exactly.
It was pointed out to me that relion_reconstruct does not use the higher order ctf parameters, which could account for the 0.1A discrepancy.