Missing Density in Local Reconstruction

Local Refinement
1

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.

2

Hi @jfz002,

Thanks for your post. When running regroup 3D, could you include a screenshot of the full inputs and parameters tab? It is likely worth running the job with “Align Pairs of Volumes” enabled (if it wasn’t already). As well, approximately what resolution do the 3D classes appear to you (by eye) and how does this compare to the resolution of the capsid?

Michael