Dear all,
from time to time, I encounter a narrow gap in the FSC curves. An example is shown in the attached image. This particular case is the result of a local refinement using a relatively narrow mask. However, I’ve observed similar features in many other datasets as well — both in local and homogeneous refinements. What could be the origin of this effect? Could it be related to issues with Cs correction, aberrations, or incorrect pixel size? Should I be concerned about it?
If only present in the final “autoadjusted” mask FSC, the autoadjust is tightening the mask too much. If you look in the CryoSPARC guide, it also discusses that is can be a phase randomisation artefact, but in my experience it’s usually the mask being too tight. Unfortunately, CryoSPARC doesn’t make the phase randomised FSC easy to access, but you can download the half maps and mask and run RELION post-processing with them; if the phase randomisation point is where that sharp dip is, you have your culprit! 
edit: Typo. 
1 Like