Ab initio failure

3D Reconstruction
1

HI all,
i am trying to run Ab initio jobs but somehow it crashes along the way. if i ask for 1 or 2 ab initio model no issue, it works. but 3 and above the job starts fine, create the right number of model sand they look Ok until a certian number of iteration where it starts to get worse then finaly fail with teh following error
[CPU: 1.84 GB Avail: 250.70 GB]
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 115, in cryosparc_master.cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/abinit/run.py”, line 288, in cryosparc_master.cryosparc_compute.jobs.abinit.run.run_homo_abinit
File “/home/bio21em2/Software/Cryosparc/cryosparc_worker/cryosparc_compute/noise_model.py”, line 119, in get_noise_estimate
assert n.all(n.isfinite(ret))
AssertionError

we are running cryosparc 4.5.1

2

I’ve run into this before, but only with non-standard parameters or unusual datasets. Is this happening with default params, on otherwise well-behaved datasets?

3

Yes standard parameters but dataset is average, relatively thick ice as particle is 55nm , contains 1M urea, 200kV, so you can imagine signal to noise could be better ! ctf fit is not great, on average 6A.
The maps goes to 4.8A.
One of the things I don’t get is why when selecting different number of models the output is either fine or crashes