ThreeDSFC job fails v4.1.2

Post Processing
1

We are trying to run a ThreeDSFC job on cryosparc v4.1.2 using as input the volume and mask resulting from a homogeneous refinement job. We have tried to vary the input parameters of the job but we always receive the same error:

Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 96, in cryosparc_compute.run.main
File “/home/lnd/Cryosparc/cryosparc_worker/cryosparc_compute/jobs/fsc3D/run.py”, line 80, in run_fsc3D
results = compute.generate_3dfsc(map_half_A, map_half_B, apix, dthetaInDegrees)
File “/home/lnd/Cryosparc/cryosparc_worker/cryosparc_compute/jobs/fsc3D/compute.py”, line 858, in generate_3dfsc
NormalizeShells(nx,ny,nz,kXofR,kYofR,kZofR,inc,retofROutR, retofROutI, n1ofROut,n2ofROut, NumAtEachR, RMax);
IndexError: index 8 is out of bounds for axis 0 with size 8

Does somebody have an idea how to fix this?

2

Same Error for my ThreeDSFC on v4.1.1.

3

Hey @Pielhaas and @shuhui, it seems to be a bug within the 3DFSC code itself, and I’m not sure why it’s only showing up now. But we will fix it on our end in a future patch :slight_smile:

4

Hi @shuhui, @Pielhaas, this should be fixed in the latest patch - let us know if there’s any further issues!

5

Thanks @kwang - further issues with 3D-FSC in this thread from a while back: 3D-FSC feature request

(see second message re missing stuff in plots)

6

Thanks for fixing this. There is yet one more issue, the volume does not display in the volume viewer

7

Thank you, @kwang, we upgrated to the newest version of cryosparc, while still with the same error when run threeDFSC as below.

[CPU: 1.13 GB Avail: 118.07 GB]
Traceback (most recent call last):

  • File “cryosparc_master/cryosparc_compute/run.py”, line 96, in cryosparc_compute.run.main*
  • File “/s0/cryosparc_user/cryosparc_worker/cryosparc_compute/jobs/fsc3D/run.py”, line 80, in run_fsc3D*
  • results = compute.generate_3dfsc(map_half_A, map_half_B, apix, dthetaInDegrees)*
  • File “/s0/cryosparc_user/cryosparc_worker/cryosparc_compute/jobs/fsc3D/compute.py”, line 858, in generate_3dfsc*
  • NormalizeShells(nx,ny,nz,kXofR,kYofR,kZofR,inc,retofROutR, retofROutI, n1ofROut,n2ofROut, NumAtEachR, RMax);*
    IndexError: index 8 is out of bounds for axis 0 with size 8
8

Have you applied the 230302 patch? You can query the patch level by running:
cat /s0/cryosparc_user/cryosparc_worker/patch