Agree 100% with @CryoEM2 . @Amy you can check this link for some useful insights: CryoSPARC Workflow Discussion: Comparing Different Processing Orders - #3 by zhe
From experience, flexible proteins demand some adaptation to the standard protocol of particle selection. Try to focus on 3D instead of 2D (hetero refinements, 3DVA, 3DFlex, 3D classification). Of course optimising the picking is important as it is expected to inflate the initial set, and if you want to reach reasonable resolution, you’ll probably need a lot of particles.
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