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​