`mscope_params/neg_stain` error message

Troubleshooting
1

Can anyone guess what this “mscope_params/neg_stain” message means?

I’m trying to do “extract from micrograph”.

As micrographs input, I entered
J113.exposures_success

and as particles input, I entered
J206.particles_selected

[CPU: 86.2 MB] Importing job module for job type extract_micrographs_multi…

[CPU: 147.4 MB] Job ready to run

[CPU: 147.4 MB] ***************************************************************

[CPU: 271.1 MB] Particles already have CTF estimates: these will not be modified.

[CPU: 271.1 MB] Traceback (most recent call last):
File “cryosparc2_worker/cryosparc2_compute/run.py”, line 82, in cryosparc2_compute.run.main
File “cryosparc2_compute/jobs/extract/run.py”, line 129, in run_extract_micrographs_multi
negative_stain = micrographs_dset.data[‘mscope_params/neg_stain’][0]
KeyError: 'mscope_params/neg_stain’Preformatted text

My current guess is that I experience some format incompatibility since I am trying to use someone else’s data which were generated by ~May of 2019 cryosparc version, while I’m using the latest version (2.14.2) now.

2

Hi @dnamkr,

You’re correct, this is a data format incompatibility. In order to get around this, you will have to run your micrographs through the “Exposure Tools” job found under the “Utilities” section in the job builder. You don’t need to change any parameters. Just connect the job, queue the job, and your micrograph dataset will be updated to the latest version. Thanks!

1 Like
3

I tested with 1 micrograph, it works. Thank you