CTF estimation error with high mag

CryoSPARC Live
1

Hi,

I am running the latest cryoSPARC Live version on a dataset with rather high magnification because we are looking at a small particle. The data is from a K3 in superres with a pixel size of ~0.2Å/px. During the live processing the motion correction step works fine, but CTF estimation fails with:

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/jobs/rtp_workers/run.py”, line 92, in cryosparc2_compute.jobs.rtp_workers.run.rtp_worker
File “cryosparc2_worker/cryosparc2_compute/jobs/rtp_workers/run.py”, line 224, in cryosparc2_compute.jobs.rtp_workers.run.process_movie
File “cryosparc2_worker/cryosparc2_compute/jobs/rtp_workers/run.py”, line 522, in cryosparc2_compute.jobs.rtp_workers.run.do_patch_ctf
File “cryosparc2_worker/cryosparc2_compute/jobs/rtp_workers/run.py”, line 523, in cryosparc2_compute.jobs.rtp_workers.run.do_patch_ctf
File “cryosparc2_worker/cryosparc2_compute/jobs/ctf_estimation/patchctf.py”, line 66, in cryosparc2_compute.jobs.ctf_estimation.patchctf.patchctf
File “cryosparc2_worker/cryosparc2_compute/jobs/ctf_estimation/patchctf.py”, line 83, in cryosparc2_compute.jobs.ctf_estimation.patchctf.patchctf
AssertionError: Get rid of patches that are too close to edges

Is there a setting I can change to make this work? Processing for datasets with larger pixel sizes works fine, so I suspect that the high magnification/small pixel size is the culprit.

Thanks,
Thomas

2

Does it fail if you manually specify the number of knots (patches)? 4 or 5, say.

3

I tried anywhere between 5 to 1 knot(s) in x and y and get the same error message. I have not tested it yet outside of the live version to see how it behaves there.

4

To follow up on this, the same error occurs in the standard version during CTF estimation. After testing a few mags and pixel sizes, it seems that anything less than 0.2A/px triggers the error (0.19 is not working 0.22 is). For what it is worth, running the CTFFIND wrapper or GCTF works fine.