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 MicAssess program to assess the quality of K3 movies. After the micrograph assessment the scripts generate a Relion star file with good micrographs to continue with the CTF job step but also a filelist for cleanup of maybe not-good movies.
MicAssess can handle float32 and float16 micrographs.
These scripts have been tested with Relion 3.1 and 4.0beta2 and MicAssess 1.0.
- 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 MicAssess software is already installed and the pre-trained model 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 MicAssess 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-micassess if you are using environment modules.
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Put the bash script relion_ext_micassess.sh to $PATH like /usr/local/bin or choose it via the Browse button in Relion.
A simple user guide can be found on Relion MicAssess integration