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

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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

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Has anyone attempted to make a script to import cryolo picks directly to crysoparc? I tried to concatenate as @olibclarke suggested without any luck.

Currently picked particles from denoised micrographs (using topaz output), which works just fine, but having issues converting them into a particle.star file that will import and link to the topaz denoising job which I ran in cryosparc. Any ideas @apunjani?

I know this is an older thread, but I since it was related to my question I did not want to open a new thread.

we just do an extraction in relion (using the .box files) and import ignoring raw data - does that not work for you @Omid?

Hi @olibclarke,

I have done it in the past but for some reason I had a hard t using the same denoised micrographs that I used for picking. Maybe it is because some of the micrographs have zero picked particles. I am sure I can figure it out using relion eventually… Just curious if someone had a script for it that they did not mind sharing which avoids going from cryolo, to relion and then to cryosparc. Perhaps I’ll set some time aside and make one. I am just very slow at scripting.

Best,
Omid

hmm - was it giving an error of some kind? I’ve been doing it with JANNI denoised micrographs without issues

Yeah it was not able to find one of the input micrographs. I suspect it is because no particles were picked for that image and hence no box file output for that corresponding micrograph. I’ll test it out later…