I am working with the filament structure which spans through the box but refinement is done in C1 symmetry. Because the density is not focused in the middle it makes problems with the local refinement (assertion error). I discovered that when the Window inner radius and Window outer radius are changed to ~0.6-0.7 the error does not occur and refinement works well. However, I noticed that the rest of the box outside the Window outer radius is not masked with 0 but there is still visible density. Is there a way to mask the volume close to the box boundaries like it is done in Relion with circular mask? Thanks!