Requesting support for cryosparc .cs file import

Import and Export
1

Hi All,

It would be helpful if we could import .cs files without first converting to a star file. Attempting to do so in cryosparc V4.7.0 produces the following error.

AssertionError: Cannot import file of type cs

Best,

Ryan

2

May I ask:

  1. How did you obtain the the *.cs file?
  2. Do you have access to the CryoSPARC project within which the *.cs was generated?
3

Sorry, maybe I should have also specified I am attempting to do this with the import particle stack job type.

  1. The .cs file was obtained from running Simulate Data in cryosparc
  2. Yes, Also, I provided the path to the simulate job folder where the .mrcs files are stored as “Particle data path”

Best,

Ryan

4

Would this be a use case for (1) exporting, then (2) importing an output group?

5

This would not be a use case for exporting and importing as an output group since the reason for importing was to manually override the pixel size. An additional use case would be when a user wishes to analyze a cryosparc formatted particle stack in an external program and re-import into cryosparc.

1 Like
6

Hey @RyanFeathers – if I understand correctly, you should be able to do this via CryoSPARC tools. You can load an output (effectively loading a cs file), modify it as necessary, and use an external job to ‘re-import the modified cs file’ (which becomes an output of an external job) with the new pixel size. See, for example, the re-centering particles code on the doc page.

1 Like
7

CryoSPARC tools, mentioned by @vperetroukhin, are now the recommended method for modifying and loading modified metadata. An older method, still available in v4.7 and based on custom CryoSPARC group (.csg) files, is described here.