A simple utility to convert cryosparc particle positions to relion star format.
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.
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
cs2star cryosparc_job_dir [dest_dir]
A couple more options are available, check out the help page with
Cryosparc/J23 is a classification job:
cs2star Cryosparc/J23 -p
will create in the working directory:
- a relion-ready
- a relion-ready
patchesdirectory containing the particle images to be used by relion refinement You can now run
micrographs.staras the inputs.
- While you can use the
--classoption 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
.staris to use the
select 2D classesjob in cryosparc, then provide this job as input to cs2star.
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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