Working with negative stain data

Import and Export
1

Hi all,

I have some negative stain data that I’ve been working with that I want to see how it gets processed in cryoSPARC however I am running into some difficulty properly importing files that I’m working with even after consulting the brief negative stain data tutorial. I have a stack of particles extracted from micrographs that I can readily import as .mrc micrographs with .box particle coordinates or as .mrc particle images. I’ve successfully imported the NSEM micrographs and as best as I can tell, CS wants me to import particle coordinates as .star files and I’m not really sure an easy way to transfer my coordinates to that.

I have tried importing the particle stacks (single .mrcs) and individual particle images (~4500 .mrc images). Both times I have been met with the following error:

    [CPU: 206.9 MB]  Traceback (most recent call last):
  File "cryosparc_master/cryosparc_compute/run.py", line 84, in cryosparc_compute.run.main
  File "/home/cryosparc_user/cryosparc/cryosparc_master/cryosparc_compute/jobs/imports/run.py", line 40, in run_import_particles
    far_import_path = os.path.expandvars(params['particle_meta_path'])
  File "/home/cryosparc_user/cryosparc/cryosparc_master/deps/anaconda/envs/cryosparc_master_env/lib/python3.7/posixpath.py", line 288, in expandvars
    path = os.fspath(path)
TypeError: expected str, bytes or os.PathLike object, not NoneType

I’m trying to figure ideally how to import the particle stacks into cryoSPARC or if there’s a convenient way to convert .box to .star coordinates and import those.

Thank you,
Russell McFarland

2

Hi @RussellM,

What value did you enter for the path parameter? The file browser should show a preview of files that will be searched by the job. Typically you would specify something like /my/folder/*.mrcs.

- Suhail

3

For the path parameter I entered basically what you have written there. I double checked to make sure that I have the absolute path entered (rather than going through symlinks) and verified that the cryosparc user account had permissions to read/write the files I’m trying to import.

4

Hey @RussellM,

Check out this post:

5

Thank you - this thread helped to me get the particles imported as a relion particle.star file and I have it working now - I was able to run classification on this particle stack.

  • Russell
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