These scripts can be called inside the Relion user interface in the External jobs section. They setup a correct Relion directory structure and call the external crYOLO particle picking software using the crYOLO generic model. This means no handpicking or training a model is required. The picked coordinates can be imported with the Relion Import function. Instructions to view and verify the picks in Relion are provided in the user guide mentioned below.
These scripts have been tested with Relion 3.1 and 4.0beta and crYOLO 1.6 up to 1.8.
- Only the pre-made crYOLO gmodel can be used so far
- Only the additional threshold parameter can be set and changed in the Relion user interface
- All MRC files in Relion are organized in a Movies or Micrographs folder. The user guide provides examples how to link movies from a complex EPU folder into this structure.
It is assumed that the Relion and crYOLO software is already installed and the crYOLO gmodel files are downloaded from the original site.
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Checkout the repository or download the bash scripts
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Decide if you run the scripts locally on a workstation or submit the crYOLO job as a job to a computing cluster. A working example from our SLURM cluster is provided.
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Adapt and add the settings from env.source file to your environment (e.g. $HOME/.bashrc). Alternatively you can adapt and copy the file env.modules to e.g. $HOME/privatemodules/relion-ext-cryolo if you are using environment modules.
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(Optional) The scripts run just with the environment settings. You can override the crYOLO calls in these cryolo_gmodel.sh scripts if needed.
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Put the bash script relion_ext_cryolo_gmodel.sh to $PATH like /usr/local/bin or choose it via the Browse button in Relion.
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(Optional) You can set your own pre-trained model instead the gmodel files in the according environment variables.
A simple user guide can be found on Relion crYOLO integration.