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.