I am running a local refinement in cryoSPARC 4.2.1, with ‘Optimize per-particle scale’ activated. It seems to help a lot, the resulting density is at higher resolution and looks reasonable.
Estimating particle scales gives this output:
The problem is that after a few iterations, I get this message in the log:
Rescaling optimal scales and reconstruction result to preserve median 1.0. Rescaling factor is nan
After this, the density disappears and the reconstruction just produces empty boxes:
Refining scales does seem unstable in local refinement.
I don’t have a solution to this really, but I wonder if you kill your job after it has done a couple of iterations (before it becomes unstable) and mark it as complete, if you could then use the output particles for a round of local refinement with fixed scales (using the scales you have already refined)?
We aren’t sure what might be causing this, but to help our investigation, could you send us (either on the forum, or via DM) the Job error report?