Guidance for exporting particles for cryoDRGN-AI

Import and Export
2

Hi, here is how I have been doing this:

  • CS refinement: depending on your workflow
  • CS Restack particles: set a batch size >= the total number of particles (gets rid of unused particles from early refinement)
  • CS Particle sets: open input card and remove location attribute, then “split” to 1 batch (makes the set portable)
  • Export Particle sets job
  • Move job directory with symlinks disabled (optional, if CS/CD are running on separate machines)
  • Downsample particles for CD: cryodrgn downsample [input particle stack] -D 128 -o particles.128.mrcs
  • Parse poses into .pkl file: cryodrgn parse_pose_csparc cryosparc_P27_J3_005_particles.cs -o pose.pkl -D 300 (where -D is your original box size)

Sources:

Hope this helps!

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