OK good to hear - I have seen better results myself sometimes with it on for non-uniform and homogeneous refinement
I am trying out the particle subtraction now, but it does not seem to be effectively subtracting the residual density (whereas signal subtraction in relion does, for the same set of particles). Is cryosparc expecting a regular mask or an inverse mask, for signal subtraction?
For troubleshooting, it would be useful if cryosparc output the volume the projections of which it will subtract from the particles, so that the user can inspect.
Cheers
Oli