Building a Working Directory

Steps to manually build an AlphaFold working directory:

• Navigate to your chosen directory (e.g., cd /scratch/$USER/alphafold)
• Make a directory to hold fasta files (mkdir fasta)
• Make an output directory to hold AlphaFold outputs (mkdir outdir)
• Make a directory to hold conda environment (mkdir conda)
• AlphaFold doesn’t output QC metrics in plot or human-readable formats. We can access this info with an add-on, alphapickle, a python package from GitHub that makes QC plots and human-readable QC metric files (.csv/.txt) from the pickle file output of AlphaFold. Install alphapickle from GitHub:

  git clone [https://github.com/mattarnoldbio/alphapickle.git](https://github.com/mattarnoldbio/alphapickle.git)

• The author has modified a python script to generate a sequence coverage plot. Put sequence_coverage_plot.py in your AlphaFold directory.

Other notes:

Sequence_coverage_plot_fxn.py is a script modified from https://raw.githubusercontent.com/jasperzuallaert/VIBFold/main/visualize_alphafold_results.py to generate sequence coverage plots by deriving info from the features.pkl file.

Outdir is an empty directory in which the output files will go.