Alphafold Working Directory

AlphaFold is available as a module on Rivanna. Load it using:

module load apptainer/1.3.4 alphafold/2.3.0

View available AlphaFold versions:

module spider alphafold

More information on available versions

Directory Contents

The alphafold directory can contain the following:

  • SLURM job scripts (*.slurm)
    Several SLURM scripts are provided for submitting AlphaFold jobs for different use cases.

  • fasta/
    This subdirectory contains the FASTA files required for both monomer and multimer AlphaFold runs.

  • conda/
    This is a Conda environment that includes the necessary Python packages for running the alphapickle utility and the sequence_coverage_plot.py script.

  • alphapickle/
    This folder contains a GitHub package used to generate human-readable quality control plots and metric files (in .csv and .txt format) as well as QC plots from the .pkl results generated by AlphaFold.

  • sequence_coverage_plot.py
    This is a custom script, modified from the VIBFold project, which generates sequence coverage plots using information from the features.pkl file.

  • outdir/
    This directory is the destination for output files produced during AlphaFold runs.

View the files in your working directory:

cd alphafold​
ls -lh​
Example of AlphaFold working directory contents
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