Hi Andy,
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If the particles are off centered, but the 2D classes are well-centered, re-extracting with recentering (which is on by default) should recenter them.
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You can do this by replacing the particles blob in the low level results with the one from the “full scale” particles - see (Initial resolution improvement, then deterioration in Non-Uniform refinement - #9 by wtempel) for an explanation of the process in another context.
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In global refinement, this is handled automatically, and I do not believe there is a way to “force” finer angular samplings. In local refinement there is an option to choose the maximum angular sampling (by default 0.2deg).
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There is no way to select based particles based on figure of merit (I guess you are thinking like Pmax in relion) in cryoSPARC, to my knowledge. You can select particles based on probability of belonging to a particular class, after 2D or 3D classification, using the Class Probability Filter job type.
Hope that helps
Cheers
Oli