A simple utility to convert cryosparc particle positions to relion star format.
Project description
cs2star
A simple utility that wraps around csparc2star.py
to convert particle positions from Cryosparc JOB directories into a RELION-ready directory. On top of what csparc2star.py
already does, this script will traverse the Cryosparc job tree to find the relevant .cs
files, automatically symlinks (or copies) the .mrc
files (renaming them as appropriate to mrcs
and updating the rlnMicrographName
column to reflect the change). cs2star
also separates micrograph information in a micrographs.star
file, which is required in several relion jobs.
Installation
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 [NOTE: some fixes necessary for this are not yet on the main repo, so we're installing from a fork]:
pip install git+https://github.com/brisvag/pyem.git
You can then install cs2star
with pip:
pip install cs2star
Usage
cs2star cryosparc_job_dir [dest_dir]
A couple more options are available, check out the help page with -h
.
Example
Assuming Cryosparc/J23
is a classification job:
cs2star Cryosparc/J23 -p
will create in the working directory:
- a relion-ready
particles.star
- a relion-ready
micrographs.star
- a
patches
directory containing the particle images to be used by relion refinement You can now runrelion
and provideparticles.star
andmicrographs.star
as the inputs.
Tips
- 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 theselect 2D classes
job in cryosparc, then provide this job as input to cs2star. --swapxy
defaults toTrue
. 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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