Hi cisTEM folks,
I'm having trouble with the mask options with Manual Refine. If I understand correctly, when one chooses a user-defined mask, the mask is applied to the volume for a given iteration and placed in the Scratch/ManualRefine3D directory. However, when I look at the volume that directory, it doesn't look like the mask that I defined is being applied. Is this a bug, or am I not understanding how to use the options properly? If it's not a bug, is there a way to get it to apply a mask each iteration?