@iswaryapj Have you tried downsampling your particles? Downsampling to a box size of 128 or even 84 results in 3DVA to speed up exponentially. Once your variability analysis is done, you can “upsample” your particles for further refinements following these instructions. Works like a charm. (Unbinning particles using 'Downsample particles' job in CRYOSPARC)
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