Depositing Particles to EMPIAR

Import and Export
1

I was searching the forum but could not find much information on what is the best method for depositing a particle stack from a final non-uniform refinement to EMPIAR? I am thinking of the following options:

  1. Export the NU-refine job and copy the entire folder

  2. Run restack particles, export the restack particles job, and copy that folder

Do you typically also deposit the motion-corrected micrographs in addition to raw movies? I was trying to export particle stacks from one workstation (using cryosparc v5) to our university HPC (cryosparc v4.7.1) but ran into an error with the particles needing the motion-corrected micrographs, and I worry that any EMPIAR user could run into a similar issue if I do not deposit the motion-corrected micrographs?

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2

Hi,

This previous post is related to this: EMPIAR deposition

What I do is to convert the .cs file into a .star file and import it that way. You lose the global CTF refinements though (but can be calculated again). It is also possible to re-connect the particles to newly calculated motion-corrected micrographs. This is a rough protocol of how I do it:
Export:

  1. Make a “particle_stacks” folder containing your final particle stacks (.mrc) from the cryosparc job.
  2. Export the final job on cryosparc, the go to folder in “exports”, then to the particle folder.
  3. Convert the cs file into star with pyem:
  • conda activate pyem
  • csparc2star.py --inverty /path/to/cryosparc/project/exports/jobs/final_job/JX_particles/JX_particles_exported.cs particles.star

Import:

  1. Import the movies and motion-correct them
  2. Import the particles (select the data folder as “particle_stacks” (where your .mrc are) and meta file the “.star” file with the motion corrected added as input as well). Change the following settings:

  • Strict check of: Particle pick locations (locations), particle raw data (blob), particle CTF parameters (ctf), particle 3D alignments (alignments3D).

  • Remove leading UID in input exposure file name

  • Length of rlnMicrographName base name prefix to cut for query : 22

  • Length of input exposure file name prefix to cut: 13 (might need to be adjusted)

    *If I am not wrong, you can also just import them without giving any micrographs, this is just if you want to re-link them. In that case, you just import with the data folder (where the .mrc are) and meta file (.star file) with the strict check mentioned.

I hope this helps.

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