Mask creation with Volume Tools job

Local Refinement
1

Hi!

I am new to cryo-EM, so, a lot of things are confusing to me. I need to improve resolution and I decided to focus on part of my volume and remove the side. So, I created the volume I want to refine according to the tutorial and imported it to CryoSPARC as volume. Then I am supposed to run Volume Tools job and convert volume to mask. I set padding to 11 according to formula (5*resolution/pixel size), and dilation radius to 6. Anyways, I run onto error:

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I would appreciate any suggestions what could go wrong, I cannot see this error for this job at the forum…

2

@opal Thanks for your post. Please can you post

  1. the error message as text instead of a screenshot, for more efficient forum text searches
  2. the output of the command (after replacing P12, J934 with the actual project and job UIDs, respectively:
    cryosparcm cli "get_job('P12', 'J934', 'job_type', 'version', 'params_spec', 'instance_information', 'input_slot_groups')"
3

Hi! Thanks for the reply.

Unfortunately, it seems I have deleted that specific job. But I have some other that have similar errors, This is one of them:

[CPU: 264.2 MB Avail: 476.64 GB]
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 95, in cryosparc_master.cryosparc_compute.run.main
File “/home/cryosparc_user/software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/utilities/run_volume_tools.py”, line 138, in run
assert n.isclose(maxval, 1.0, atol=1e-4), “Output mask maximum value is not 1! Are you sure the output type is intended to be a mask, not a map?”
AssertionError: Output mask maximum value is not 1! Are you sure the output type is intended to be a mask, not a map?

the command is:

cryosparcm cli “get_job(‘P16’, ‘J534’, ‘job_type’, ‘version’, ‘params_spec’, ‘instance_information’, ‘input_slot_groups’)”

4

also, one of the jobs, Volume Tools to convert volume to mask, gives an error:

[CPU: 220.4 MB Avail: 476.29 GB]
Traceback (most recent call last):
File “cryosparc_master/cryosparc_compute/run.py”, line 95, in cryosparc_master.cryosparc_compute.run.main
File “/home/cryosparc_user/software/cryosparc/cryosparc_worker/cryosparc_compute/jobs/utilities/run_volume_tools.py”, line 63, in run
input_shape = volumes_dset[volume_type+‘/shape’][0]
TypeError: ‘NoneType’ object is not subscriptable

5

What is the screen output when you run

cryosparcm cli "get_job('P16', 'J534', 'job_type', 'version', 'params_spec', 'instance_information', 'input_slot_groups')"

and the output corresponding get_job() command command for the other job you mentioned

6

Hi! I am a beginner and I am run CryoSPARC from GUI, I need to look into it to run it from the command line…

7

Please see this guide section.