Resolution mismatch homo refine & local CTF refine

I would like to understand the following resolution mismatch between the output of homo/helix refine and the input of downstream jobs like local resolution or local CTF.
In this example of EMPIAR-10020 the polished, global&local CTF refined FSC(0.143) resolution is 3.0 Ang after helix refine.
When I do downstream processing from this job, in this case a second round of Local CTF Ref, CryoSPARC will use the same half maps and FSC masks for another round of resolution determination, this time with a higher value of 3.12 Ang
My question is: Why are they not the same?

  • the “No Mask” values are the same
  • the new “Masked” FSC does not match any of the masked FSCs after mask auto-tightening, but looks very similar to the “corrected” curve before auto-tightening


CryoSparc v4.4.1+240110
RockyLinux 9.3 (Blue Onyx)
RTX20XX, 30XX and 40XX GPUs


When selecting a mask result group as input for downstream jobs, IIRC cryoSPARC defaults to mask_refine in the input slot, so perhaps this tracks with what you’re observing. Of course, you can choose to replace the input slot with a different mask using the low-level interface.


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