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 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 https://github.com/asarnow/pyem.git 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
Cryosparc/J23 is a classification job:
cs2star Cryosparc/J23 -p
will create in the working directory:
- a relion-ready
patchesdirectory containing the particle images to be used by relion refinement You can now run
particles.staras the input.
- 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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