The particles I am working with are filaments with non-constant contrast, basically a stack of dimers, with each dimer separated from the other by a low-density interface. I want to reconstruct the interface and having trouble with cryoSPARC.
Through each steps up to and including ab-initio reconstruction, I can keep the focus on the interface by disabling the recenter option. When it comes to homogenous refinement, cryoSPARC starts nicely refining the interface, but then it always ends up shifting the map to the dimer. I tried masking, reducing the window inner and outer radius, changing the dynamic mask, centering on a monomer… Nothing worked. How do I stop cryoSPARC refinement from translating the particle?