Greetings,
I was trying to run a NU-refinement with
refine_scale_min
refine_defocus_refine
refine_ctf_global_refine
and got the following error message:
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 115, in cryosparc_master.cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/refine/newrun.py”, line 533, in cryosparc_master.cryosparc_compute.jobs.refine.newrun.run_homo_refine
File “cryosparc_master/cryosparc_compute/jobs/refine/newrun.py”, line 534, in cryosparc_master.cryosparc_compute.jobs.refine.newrun.run_homo_refine
File “cryosparc_master/cryosparc_compute/jobs/ctf_refinement/run.py”, line 185, in cryosparc_master.cryosparc_compute.jobs.ctf_refinement.run.full_ctf_refine
AssertionError: The maximum CTF Refinement fit resolution of 15.89 Angstroms is worse than the minimum Global CTF Refinement fit resolution parameter of 10.00 Angstroms.
This indicates resconstruction quality is not high enough to confidently perform CTF Refinement.
If this is a Homogeneous or Non-Uniform refinement job: please mark the job as complete, or run the job without Global CTF Refinement enabled.
CTF Refinement can be attempted subsequently by running the standalone Global CTF Refinement job.
If this is a standalone Global CTF Refinement job, consider setting a lower (i.e. worse) Minimum fit resolution and/or a higher (i.e. better) Maximum fit resolution.
Since the resolution is still trapped at 10 A and I’m not expecting it to be better than 5 A anyway, I thought Global CTF won’t do much and instead ran a standalone Local CTF Refinement instead. It turned out to be awful, confusing and also with an error:
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 115, in cryosparc_master.cryosparc_compute.run.main
File “cryosparc_master/cryosparc_compute/jobs/ctf_refinement/run_local.py”, line 153, in cryosparc_master.cryosparc_compute.jobs.ctf_refinement.run_local.run
File “cryosparc_master/cryosparc_compute/jobs/ctf_refinement/run_local.py”, line 236, in cryosparc_master.cryosparc_compute.jobs.ctf_refinement.run_local.full_defocus_refine
File “cryosparc_master/cryosparc_compute/jobs/ctf_refinement/run_local.py”, line 344, in cryosparc_master.cryosparc_compute.jobs.ctf_refinement.run_local.do_defocus_refine
IndexError: list index out of range
This is really shocking so I double checked my micrographs with a Manually Curate Exposures job. But things seems OK to me?
Most of the exposures do have a CTF fit resolution greater than 5 A though, is this likely the cause of issue? Feeding the Local CTF refined particles back into refinement jobs doesn’t improve the issues either. Is there any thing I can do at this stage to try to utilize this data set?
Many thanks in advance.
Iz
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