Nan error in 3D variability

I am getting the following error while running 3D variability:

[CPU: 7.63 GB]   Traceback (most recent call last):
  File "cryosparc2_worker/cryosparc2_compute/", line 85, in
  File "cryosparc2_worker/cryosparc2_compute/jobs/var3D/", line 533, in
  File "cryosparc2_worker/cryosparc2_compute/jobs/var3D/", line 445, in
  File "/users/svc_cryosparc/software/regular/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/numpy/linalg/", line 1058, in eigvals
  File "/users/svc_cryosparc/software/regular/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/numpy/linalg/", line 218, in _assertFinite
    raise LinAlgError("Array must not contain infs or NaNs")
LinAlgError: Array must not contain infs or NaNs

It happens in somewhat random iteration have seen it happening in iteration 5, 6 and 8 in different trials. I tried different queues.

The dataset however behaves fine and refines nicely in 3D refinement. Any idea?



It seems fairly erratic I got a job running through after quite a few trials.

@david.haselbach which version of cryoSPARC was this?

It is the 2.16 beta version


I have Nan error in 3D variability as well and it happens at iteration 2. I am trying to repeat the 3D variability analysis based on the recent paper of Key Lewis “Probing cooperativity of N-terminal domain orientations in the p97 molecular machine: synergy between NMR and cryo-EM. Rui Huang, Zev A Ripstein, John L Rubinstein, and Lewis E.Kay 2020” but I have a problem at 3D variability. I checked the version of the cryoSPARC they used and I am using the same version. According to the paper, I made volume out of the PDB files and then using a simulated data job I got the particle images and did the refinement. First I tried the 3D variability using the particles and mask from C6 refinement and it seems fine but when I put a mask on N domain as it is described in the paper with and without expand symmetry I get the attached error. Could you please let me know what am I doing wrong?