The particles (inverted and normalized) are picked in Warp are imported in cryosparc and feeded into 2D class with the following error.
I was running a 2D class in cryosparc with the following error output:
[CPU: 2.85 GB] Traceback (most recent call last): File "cryosparc2_compute/jobs/runcommon.py", line 1547, in run_with_except_hook run_old(*args, **kw) File "cryosparc2_worker/cryosparc2_compute/engine/cuda_core.py", line 110, in cryosparc2_compute.engine.cuda_core.GPUThread.run File "cryosparc2_worker/cryosparc2_compute/engine/cuda_core.py", line 111, in cryosparc2_compute.engine.cuda_core.GPUThread.run File "cryosparc2_worker/cryosparc2_compute/engine/engine.py", line 1072, in cryosparc2_compute.engine.engine.process.work File "cryosparc2_worker/cryosparc2_compute/engine/engine.py", line 392, in cryosparc2_compute.engine.engine.EngineThread.find_and_set_best_pose_shift ValueError: invalid entry in index array
What I found suspicious that the particles did not look inverted (they look dark-on-white) while I defined them as light-on-dark (according to Warp). In the import I defined Amplitude Contrast (fraction) as the absolute dose (e.g. 43.57) but I am not sure if this was correct. Its rougly 360000 particles and I wanted a rough first classification with 100 classes, defined a mask of 320 A with an expected particle of 250 A, else I used the standard parameters.
Does anyone have an advice? Maybe I defined something wrongly?
Thanks a lot!