When I did Particle Subtraction, Volume Alignment Tool to centered on a mask and then Downsample Particles (crop to smaller size). The job failed.
Traceback (most recent call last): File "cli/run.py", line 106, in cli.run.run_job File "cli/run.py", line 211, in cli.run.run_job_function File "compute/jobs/extract/run.py", line 836, in compute.jobs.extract.run.run_downsample_particles AssertionError: Particles must all have the same alignment pixel size. If multiple particle stacks were input into the job, please instead run separate downsample jobs for each particle stack.
Apparently, if you deleted the Alignment2D from the input particles, then it worked.