[3dem] NaNs error in 3D variability job in cryoSPARC

[Sepideh Valimehr]

Dear all,

I have NaNs error in 3D variability in cryoSPARC . 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 got this error:
Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in
cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/var3D/run.py”, line 533, in
cryosparc2_compute.jobs.var3D.run.run
File “cryosparc2_worker/cryosparc2_compute/jobs/var3D/run.py”, line 445, in
cryosparc2_compute.jobs.var3D.run.run.M_step
File
“/home/sepideh/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/numpy/linalg/linalg.py”,
line 903, in eigvals
_assertFinite(a)
File
“/home/sepideh/software/cryosparc/cryosparc2_worker/deps/anaconda/lib/python2.7/site-packages/numpy/linalg/linalg.py”,
line 217, in _assertFinite
raise LinAlgError(“Array must not contain infs or NaNs”)
LinAlgError: Array must not contain infs or NaNs
 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 refinement and it seems fine but when I put a mask on N domain as it
is described in the paper  I got the error.
I posted the error in cryoSPARC forum but I didn't receive any answer.
Could you please help me to solve the problem?

Thank you in advance for your help,
Sepideh

-- 

*Sepideh Valimehr*

*Graduate Researcher *I* Rouiller Lab*

Department of Biochemistry and Molecular Biology

Bio21 Molecular Science & Biotechnology Institute

The University of Melbourne

*T:* +61 3 83440285 | *E:* sepideh.valimehr at student.unimelb.edu.au
<ashish.sethi at unimelb.edu.au>
*I acknowledge the Traditional Owners of the land on which I work, and pay
my respects to the Elders, past and present.*
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