Per particle scale error: Rescaling factor is nan

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)?


Hi @shuber,

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?