I'm puzzled with the selection between global search and local refinement in mnaual refine.
(1) If I'd like to do global 3D classfication, should I choose global search or local refinement? One published paper in your lab (http://grigoriefflab.janelia.org/sites/default/files/Zhang_Ultramicroscopy2019.pdf) suggested to use global search, but you also suggested to choose local refinement shown in your previous post (
|How to run 3D classification correctly and get particles from 3D classification|
(2) If I'd like to push resolution subsequent to autorefine, should I choose global search or local refinement in the further manual refine? No detailed clarification on this point is present in the manual (If time permits, users are strongly encouraged to try to improve their reconstructions using Manual Refine. For example, starting from the last result of auto-refinement, try to run a few more (3-5) refinement cycles using a slightly higher resolution limit. For example, if auto-refinement used a resolution limit of 5.0 Å in the last cycle, try manual refine with a Hi-Res Limit of 4.5 Å. Be careful not to come too close to your current estimated resolution! Remember the FSC is only unbiased beyond the Hi-Res Limit). It seems that autorefine only involves global search and refinement.
Looking forwards to your response and thanks for your time!