Particle coordinate transfer from one CS project to another

Import and Export
1

Dear colleagues,

I have a CS project with a non-uniform 3D refinement results.

How can I extract the particle coordinates and import them into another cryosparc project?

Thank you in advance.

Kind regards,
Dmitry

2

Do the export/import of jobs or results meet your requirements?

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3

Thank you @wtempel I will give a try. In fact from one project I have only particles.cs file. I hope that is enough.

Kind regards,
Dmitry

4

it would be nice to have “Import/export coordinates” script to continue using CS after working in relion, eman etc.

Sincerely,
Dmitry

5

Did you consider the Import Particle Stack job for this purpose?

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6

Dear @wtempel and colleagues,

I want to transfer particle coordinates from one CryoSPARC instance to another to re-extract particles using already transferred micrographs and repeated motioncor/ctf estimation steps on the second instance.

On the source workstation, I downloaded the folder ---- /data/xxx/cryosparc/CS-xxx/exports/groups/J127_particles/

that contains the following folders
J2
J126
J127_particles_exported.cs
J127_particles_exported.csg

On the target workstation, I placed this file at:

/data/xxxx/cryosparc/CS-xxx/imports/groups/J127_particles/
J2
J126
J127_particles_exported.cs
J127_particles_exported.csg

In the Import Particle Stack job, I set the Particle meta path to that folder. The job fails with:

AssertionError: Cannot import file of type cs

Can you please clarify:

  1. What is the correct folder and file structure expected?
  2. Is it possible to import just the particle coordinates (no .mrcs) for re-extraction?
  3. Can this be done without using the CLI?

CryoSPARC v4.6.0 on both systems.

Thanks for your help.

Kind regards, Dmitry

7

Did you consider a different job type, Import Result Group, for this task?

Additionally, please also consider, based on your storage arrangements, the potential need to dereference symbolic links within the data transfer workflow.

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8

Hello @wtempel ,

Thank you for your response.

Let me sum up the steps so that you can evaluate and them.

  1. Export the Particle Group (Old Machine)
  • In CryoSPARC, go to your finished particle job.
  • Click the “Export” button for the particle output.

  1. Transfer the Exported Folder to the New Machine

  2. Install cryosparc-tools (New Machine)

  3. Remove References to Missing Stack Files from .cs

  4. Edit the .csg File to Point to the Cleaned .cs

  5. Import into CryoSPARC (GUI, New Machine)

  • Create an “Import Result Group” job.
  • Input the edited .csg file.

  1. Reassign Particles to Micrographs

  2. Extract Particles

Is that the correct workflow, or is it wrong and/or am I missing anything?

Thank you

Kind regards,
Dmitry

9

Hi @Dmitry! Currently, the easiest way of transferring particle coordinates between CryoSPARC projects is to

  1. Export the job with particles you want to transfer
  2. Use pyem’s csparc2star.py to convert the .cs file to a .star file
  3. Use Import Particle Stack in the second project to import the .star file. If you turn on the Ignore raw data parameter, the .mrc files will not be imported, only the particles’ locations, CTF estimates, poses, etc.
  4. Use Reassign Particles to Micrographs to reassign the particles to the exposures in the second project
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10

@rwaldo many thanks!

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