Error in 3D variability job

3D Variability Analysis
1

Dear All,
sorry if this has been asked already but I did not find it yet here.
I get this error when I run a 3D variability job, with particles coming from a NU refinement job, and a mask I made using the final volume of that refinement job as template, where I deleted the micelle.
Here is the error:

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main (/home/installtest/deps_manage/cryosparc2_package/deploy/stage/cryosparc2_worker/cryosparc2_compute/run.c:3954)
File “cryosparc2_worker/cryosparc2_compute/jobs/var3D/run.py”, line 131, in cryosparc2_compute.jobs.var3D.run.run (/home/installtest/deps_manage/cryosparc2_package/deploy/stage/cryosparc2_worker/cryosparc2_compute/jobs/var3D/run.c:11753)
File “cryosparc2_worker/cryosparc2_compute/engine/newengine.py”, line 592, in cryosparc2_compute.engine.newengine.EngineThread.setup_current_poses_and_shifts_from_alignments (/home/installtest/deps_manage/cryosparc2_package/deploy/stage/cryosparc2_worker/cryosparc2_compute/engine/newengine.c:13288)
AssertionError: psize in alignments not the same as comparison size!

Thanks a lot for your help,
Jacopo

2

I can add that the same error appears when I use as input particles and mask coming from a standard refinement job. Could someone say what is “comparison size” ?

Thank you
Jacopo

3

Hi @marino-j,

Thanks for reporting.
“comparison size” is the size at which the reconstruction is performed (3D Var uses some new codepaths that allow for various on-the-fly scaling/cropping/downsampling operations).
For 3D Var in v2.9, the input particles must have been aligned using a box size that is the same as the box size of the particles themselves. So for example if you do a refinement but set the reconstruction box size to a smaller value (which will do on-the-fly Fourier cropping of particles during refinement) then those outputs can’t be used in 3D Var right now. You can either use the downsample particles job to Fourier crop the particles to the same box size that you used for the refinement, and then take those particles in to 3D Var, or you can re-run the refinement without specifying a reconstruction box size (which would cause the refinement to use the full particle size).

1 Like
4

Thank you for the clarification. Indeed that was the problem, particles were no Fourier crop.

Cheers
Jacopo