Hi,
I’m trying to run a local reconstruction of a small protein bound to an icosahedral capsid surface. I’ve isolated out the region I’m interested in and run 3d classification on a set of subparticles. The classes all look good. However, when I attempted to regroup the classes they resulted it resulted in a map that’s missing the central region of interest. I went back and used align 3d to align the classes to each other and the resulting reference map is exactly what I expect to see. However when I move these into local refinement, they once again are missing the central region of interest. I’m not sure if my subparticles set doesn’t contain enough data, or if I have a parameter wrong. Any help would be greatly appreciated.