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A simple utility to convert cryosparc particle positions to relion star format.

Project description


A simple utility that wraps around to convert particle positions from Cryosparc JOB directories into a RELION-ready directory. On top of what already does, this script automatically symlinks (or copies) the .mrc files, renaming them as appropriate to mrcs and updating the rlnMicrographName column to reflect the change.


This package requires pyem, which is not available on pip under that name (there is a pyem on pip; that's a different package!). To install it manually:

git clone
cd pyem
pip install -e .

You can then install cs2star with pip:

pip install cs2star


cs2star cryosparc_job_dir [dest_dir]

A couple more options are available, check out the help page with -h.


Assuming Cryosparc/J23 is a classification job:

cs2star Cryosparc/J23 -p

will create in the working directory:

  • a relion-ready
  • a patches directory containing the particle images to be used by relion refinement You can now run relion and provide as the input.


  • While you can use the --class option to select specific classes from a cryosparc job, the class indexes do not correspond the the class order in Cryosparc (which is simply based on particle number). A much easier way to select specific classes to convert to .star is to use the select 2D classes job in cryosparc, then provide this job as input to cs2star.
  • --swapxy defaults to True. This is because usually that's what you need; unfortunately, this may differ on a case by case basis, so make sure to check the data after conversion with you favourite viewer to ensure that particles are correctly centered.

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