Importing particle coordinates from one workstation to another (processed by cryoSPARC)

Import and Export
1

Dear colleagues,

I have a *star file containing particles result that were processed on workstation #2.
Can I import and re-extract these particles on workstation #1 using the coordinate *star file from workstation #2?
The input micrographs, motion correction, and CTF estimation files are the same on both workstations.

Thank you in advance.

Kind regards,
Dmitry

2

Yes, link the exposures when you import the particle .star file (else no coordinates will be saved) and check “ignore raw data” (or whatever it is exactly) so you don’t have to copy the particle stacks.

1 Like
3

thank you, Daniel.

I tried this option but still getting the following error -

Unable to queue P13 J291: ServerError: Failed to enqueue P13 J291 (import_particles): Job has builder errors. Particle meta path: Specified file does not exist.

Do you think something is wrong with my star files?
As input I am using the location of *.star files

image
image255Ă—753 21.4 KB

image
image1530Ă—752 100 KB

Thank you.

Kind regards,
Dmitry

4

Hi @Dmitry! It looks like you’re trying to import multiple star files, which currently is not supported by CryoSPARC. You could combine them using relion_star_handler, if you have RELION available.

May I ask how these STAR files were generated?

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5

Hello @rposert, I must clarify the details, but they are the cryoSPARC particles coming from the cryoSPARC project. My colleague and I ran the projects with the same micrographs, so we want to share the outcome results.
What could you recommend in that case?
Our understanding was that one could export the particle location, and another could just re-extract them from his project since the micrographs were identical.

Thank you in advance.

Kind regards,
Dmitry

6

Hi @Dmitry!

Have you tried exporting the job which created the particles, and then importing it to the second workstation using Import Result Group and the resulting .csg file? That is how I often share results between projects or instances!

1 Like
7

Hello @rposert,
Thank you. I will ask my colleague to prepare the files in the above-mentioned way.

So, there is currently no option to have particles from the cryoSPARC volume, export them as *star to the other workstation, and then import and re-extract them, right?

Thank you.

Kind regards,
Dmitry

8

When you say *star, if you mean the setup you have above (with a .star file for each micrograph), then no, that is not currently possible. However, if you have a single .star file listing all particles and their metadata (like those produced by csparc2star.py) then you can import them using Import Particle Stack!

1 Like