Dear colleagues,
After running the FSC validation I am expectedly received a better FSC but a bit worse resolution.
The output file for the FSC validation is the mask only.
So my questions is what count as a final result?
I mean what shall I report as a result:
the maps from the 3D refinement +
mask from FSC validation +
FSC curve from FSC validation?
Thank you!
Sincerely,
Dmitry
Hi @Dmitry,
The “Validation (FSC)” job will compute the FSC curves using various different masks; the ones of interest are likely the unmasked fsc (labelled fsc_nomask), and the fsc using the input mask (labelled fsc_tightmask). These will be in a text file, which can be downloaded by clicking on “[txt]” above the FSC plot. There are also other masks used to compute different curves (spherically masked, and loose masked). The specific point at which each curve crosses the 0.143 threshold is written in the legend of the plot.
Since FSC depends (heavily) on the mask used, this is why the FSC plots between the refinement job and the validation job will be slightly different. If you want to use the same mask that is associated with the final FSC plot in the refinement job, this mask is labelled in the outputs as fsc_mask_auto and can be connected to the validation job to produce the same plot. Unfortunately the meaning of resolution can be ambiguous due to its dependence on the mask.
I think for something like an EMDB upload, it’s recommended to provide the refinement half-maps, the mask used for computing the FSC curve, and the curve itself, so that anyone can reproduce it. When it comes to conventions regarding how final results are reported in a publication, however, I can’t provide much more information as it may depend on the specific journal. I hope this clarifies exactly what cryoSPARC reports as the resolution and how it can be used downstream.
Best,
Michael