I am getting artefactual FSCs when running the homo_refine programme. It is the artefact common when masking too tightly i.e. the corrected FSC drops to zero at the resolution of phase randomisation.
I tried supplying my own refinement mask rather than the dynamic one made by the programme and the problem persists. It appears that the mask used to calculate the FSC is different to the user provided one (…mask_refine.mrc vs …mask_fsc.mrc).
Would it be possible to build in a feature to use a user provided mask for fsc calculation or an advanced parameter to tweak the tightness of the mask made to calculate the fsc?
This artefact is limiting the resolution of my refinement, as it lowers the resolution of the data used for the next round of refinement.