How to understand this GSFSC

This sort of FSC is due to masking artefacts caused by the mask generated by the FSC calculation algorithm. You would get the same artefact in RELION if you provided a mask that was too tight. RELION provides a warning message when you get that, however cryosparc does not.

I have previously asked about this: Artefactual FSC in homo_refine

A solution can be to provide a mask manually or to drop the threshold for the dynamic masking. I have gone as low as 0.05. A good idea would be to look at your map.mrc file as well as the mask files (both mask_refine and mask_fsc) and see if the masks are cutting your protein density.

I believe my problem is disordered protein density at the surface of my molecule. Could this be an issue for you also?

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