Importing crYOLO particle coordinates into cryoSPARC

Currently, I’m trying to import particles picked using crYOLO into cryoSPARC. Initially, I use crYOLO to pick particles from the patch motion correction job’s output (the dose-weighted aligned micrographs). crYOLO outputs a list of star files with the particle coordinates for each micrograph. From this point on, I’m unsure of how to be using the ‘Import Particle Stack’ job to be importing those coordinates into cryoSPARC.

This is what I have tried so far with Import Particle Stack:

  1. Importing source micrographs from an earlier patch motion correction job
  2. Selecting ignore raw data and setting particle data path to all the star files outputted by crYOLO
  3. Setting the 2 suffix cuts to their correct values

This fails due to lacking, I think, the Particle meta path. But I’m not sure what the meta path for the particles should be here. crYOLO does not output any such files. What should I do in this case so that the particles can be imported successfully?

Have you tried just concatenating all the per-mic crYOLO star files together into one big particle star file (removing all except the first header of course) - that should work I would think?

Cheers
Oli

Thanks @olibclarke for the suggestion - that should work. @kmzaw please let us know if you were able to import successfully!

That did work! Thanks @olibclarke

1 Like

Hi, I am also trying to do this but still got an error that says “Could not import star file: too many fields missing” Does your star file looks like this?
Screen Shot 2021-04-30 at 2.07.34 PM|225x499

Hi Smona, the other way to do it (which I have been doing recently) is just to do an extraction in relion (using either crYOLO box or star files) purely to generate a particle star file, then import the resulting star file into cryosparc, with ignore raw data on. Maybe give that a try?

Cheers
Oli

1 Like