Gctf wrapper fails with micrograph input [Bug]

Troubleshooting
1

Hi, I tried the new Gctf wrapper in v2.4, but it failed, complaining I need to provide it with movies, even though I only selected micrograph input (and I provided it with imported micrographs as input).

I imported micrographs aligned outside of CryoSPARC, which has worked fine in the past when using the CTFFIND wrapper.

Cheers
Oli

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1 Like
2

Thanks for reporting this @olibclarke, we are looking into it!

1 Like
3

Hi,
I tried performing gctf estimations on aligned micrographs in cryosparc (v2.4) and after having experienced the same input error as mentioned above by olibclarke (about micrographs vs movies), cryosparc was updated to the latest version - v2.4.6. However, I still get the same error…

Naduni

4

Hi,

Is it possible if you can run the following command on your command line:

cryosparcm cli "refresh_job_types()"

This will dynamically reload the job builder for all jobs. It’s possible the previous builder is still cached in memory.

5

That seems to have fixed, it, thanks @stephan!

Cheers
Oli

6

@stephan I tried this and it seemed to have taken care of the old problem but I get a new error now:

Traceback (most recent call last):
 File "cryosparc2_worker/cryosparc2_compute/run.py", line 78, in cryosparc2_compute.run.main
 File "cryosparc2_compute/jobs/ctf/run.py", line 314, in run_ctf_estimation_gctf
  if not n.isclose(params['ac'],micrographs_dset.data['ctf/amp_contrast'][0]):
  ValueError: no field of name ctf/amp_contrast

I am using default parameters for amp contrast.