I am just curious about how you apply the mask in the refinement step. What does window inner radius and window outer radius stand for respectively? Do you use a Guassian curve or cosine curve to make a soft mask? Does the window inner radius stand for the starting position of the cosine curve and the window outer radius stand for the ending position of the cosine curve?
Here’s a cut-and-paste from a methods section of a paper:
Masks are prepared automatically in cryoSPARC by binarizing the map, extending the edges of the resulting shape by a set distance, and tapering the mask to 0 over a second fixed distance with a cosine edge. Similar to RELION (Scheres, 2012), cryoSPARC measures and corrects for the effects of masking by randomization of high-resolution phases as described previously (Chen et al., 2013). The mask correction process introduces a dip in the corrected FSC at the resolution where randomization begins in the calculation. The final tight masking conditions were determined automatically by cryoSPARC by adjusting the extension and fading distances of the mask to optimize the reported resolution without introducing correlation from the mask.