Motion Correction error for a particular micrograph

[Saif]

Hi
I am facing an issue with Motion Correction. It gets stopped exactly after 787th movie with the follow error. Any help regarding how to resolve the issue will be greatly appreciated.

Traceback (most recent call last):
File “cryosparc2_compute/jobs/runcommon.py”, line 1490, in run_with_except_hook
run_old(*args, **kw)
File “/mnt/raid0/bfl-group/Saif/cryosparc3/cryosparc2_worker/deps/anaconda/lib/python2.7/threading.py”, line 754, in run
self.__target(*self.__args, **self.__kwargs)
File “cryosparc2_compute/jobs/pipeline.py”, line 153, in thread_work
work = processor.process(item)
File “cryosparc2_worker/cryosparc2_compute/jobs/motioncorrection/run_patch.py”, line 118, in cryosparc2_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
File “cryosparc2_worker/cryosparc2_compute/jobs/motioncorrection/run_patch.py”, line 123, in cryosparc2_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi.motionworker.process
File “cryosparc2_compute/blobio/mrc.py”, line 114, in read_mrc
data = read_mrc_data(file_obj, header, start_page, end_page, out)
File “cryosparc2_compute/blobio/mrc.py”, line 77, in read_mrc_data
data = n.fromfile(file_obj, dtype=dtype, count= num_pages * ny * nx).reshape(num_pages, ny, nx)
ValueError: total size of new array must be unchanged

Outputting partial results now…

Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 78, in cryosparc2_compute.run.main
File “cryosparc2_worker/cryosparc2_compute/jobs/motioncorrection/run_patch.py”, line 312, in cryosparc2_compute.jobs.motioncorrection.run_patch.run_patch_motion_correction_multi
AssertionError: Child process with PID 15784 has terminated unexpectedly!

Many thanks in advance
Saif

[olibclarke]

Looks like you have one corrupted movie - if you look at this one in relion_display, or using IMOD, does it look normal? is it approx the same size as your other movies?

[Saif]

Hi, thanks for your reply.
When I processed the same data in relion, it was fine. But yes you are right, looks like few micrographs are just not good.

Any suggestion please how to fix it?

Kind Regards
Saif

[Saif]

Hi
I have deleted that particular micrograph and running motion correction again.

I would like to share with you one more thing.

I have attached an image of ribosome 3D model. This model is a complex of ribosome and 199-base long RNA. In the image you will see string of RNA is coming from the ribosome (if I am not overestimating) but when I see the refined model, I don’t see any density for this extra RNA.

Is there any way to extract, refine particles with a bigger mask in order to see the extra density? OR any other way to focus classification that you could kindly suggest, that will be highly appreciated.

Kind Regards
Saif