I got a tricky problem here with cryoSPARC 2.14.
Here’s what I did
- Import movies, patch motion alignment, patch ctf (pixel size 1.37)
- Import a prealigned particle stack from Relion with some mrcs to trick cryosparc for importing. The euler got imported & also the micrographs get connected.
- I don’t refine the imported particle stack but perform Extract particles from micrographs, and fourier cropping to 1.745 (402 pixel box size). Now the newly extracted particles has all the previous alignment data from the imported stack.
- Local refinement work well of the extracted particle stack and imported reference/mask, resulting at 4.6 A resolution.
- When I proceed to Local cTF refinement, using the extracted particles stack, resulting volume and mask (all at 402 pixel box size and 1.745 A/pixel), I got the following error
[CPU: 1.73 GB] Traceback (most recent call last): File "cryosparc2_worker/cryosparc2_compute/run.py", line 82, in cryosparc2_compute.run.main File "cryosparc2_worker/cryosparc2_compute/jobs/ctf_refinement/run_local.py", line 156, in cryosparc2_compute.jobs.ctf_refinement.run_local.run File "cryosparc2_worker/cryosparc2_compute/jobs/ctf_refinement/run_local.py", line 182, in cryosparc2_compute.jobs.ctf_refinement.run_local.full_defocus_refine File "cryosparc2_worker/cryosparc2_compute/jobs/ctf_refinement/run_local.py", line 346, in cryosparc2_compute.jobs.ctf_refinement.run_local.do_defocus_refine File "cryosparc2_worker/cryosparc2_compute/engine/newengine.py", line 649, in cryosparc2_compute.engine.newengine.EngineThread.setup_current_poses_and_shifts_from_alignments AssertionError: psize in alignments not the same as comparison size!
Looking at the previous discussion, it was because there is a difference between reference & particle box size. However, in this case, it is exactly the same. Can you explain what went wrong here?