At present, I seem to get nonsense results when applying 3D-VA to particles after local refinement. I am using the mask and particle set output by local refinement.
The mask seems to be centered in the box, but the intermediate reconstructions generated during 3D-VA have the original centering used during homogeneous refinement - that is, they don’t take account of the offset applied by the fulcrum during local refinement.
Is this expected? I guess one way around this is to just repeat local refinement, but using a fulcrum corresponding to the center of the box?
Cheers
Oli