I am trying to troubleshoot some artefacts that I see when using Local Refinement. I have noticed two problems which may be related:
Around iteration 2 or 3, there is a strong rippling effect (alternating positive and negative signal) that is apparent in the real space slices, around the boundary of my mask. This is apparent in the real space slices and not in the masked slices, so perhaps it isn’t actually a problem.
Usually the highest magnitude signal in my finished map comes from noise in the form of radial streaking around the edges (where there is likely no protein or ordered solvent). In some cases I have also seen an artificially inflated gold-standard FSC curve which I can only guess is due to this streaking effect, since the map itself ends up being largely degraded. My consensus maps do not have this streaking so I don’t think this is a result of excessive bad particles.
Has anyone had any success working around similar issues?