Hi @adtaheri,
To confirm, do you mean that you opened the cryosparc_PXX_JXX_component_0.mrc
file from a 3D Var job, rather than the volume series from a 3D Var Display job?
This file is actually the variability component, rather than an actual density map from a certain set of particles - it represents the change in density vs. the consensus refinement that was used as input for 3DVA.
Can you try using the 3D Var Display job, set the mode to ‘intermediates’ ? It will perform reconstructions from subsets of the particles. See if any of the reconstructions along component 0 look like a better resolved version of your protein.