Outputs

After running AlphaFold, your output directory will include a mix of files from different sources:

  • The .csv, .txt, and .png files are generated by AlphaPickle.
  • .pdf files typically come from the sequence_coverage_plot_fxn.py script.
  • All other files — including .pdb, .pkl, .json, and the msas/ directory — are outputs from base AlphaFold.

Files labeled ranked_0 represent the best-ranked model based on AlphaFold’s internal confidence scoring.

Example output directory
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