Dear RELION developers,
I am doing a helical refinement and noticed a warning happening once during the early stage of refinement (FSC dipping below 0.5 and rise again), although not persistent. But when I plotted the final FSC (unmasked), I did see a dipping around 0.5 A (although it might not affect the resolution estimate after postprocessing since the inflation caused the dipping at higher FSC?) I am wondering how this FSC dipping will affect the final map? Will it cause the wrong weighting when applying the Wiener filter (since SSNR is estimated from FSC, I assume)?I am doing a helical reconstruction, so I used 90% of the box size as a mask, plus a cylindrical mask (100 A) and the diameter of my filament is ~65 A. Is this mask still too tight? I do have some random small particles in the background (not ice contamination, but other proteins). Could this be the reason since the solvent is not technically flat (I tried avoid those particles during manual picking, but may not guarantee a total clean background)?
Yangqi
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