Page Comparison

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• --mutations-file

  • Tab Separated Value (TSV)-formatted file containing mutations. To create an empty mutations file from an input PDB, run:

    Code Block
    cyrus engine prepare mutations <pdb-file> --output-dir <output-dir>

  • Each row can contain one or many mutations, in the format D or DMG. For example, The TSV file below would run DDG on M1D, M1G and Q2T and would report scores for all 3 of those mutations. The mutations are performed separate from each-other (ie the M1D and M1G mutations are not performed at the same time.)

  • Do not supply the native residue as a mutation, that doesn’t make sense.

    Code Block
    position original_residue mutation 1 M DG 2 Q T

• --mult-mutations-file

  • TSV file containing mutations to run simultaneously. Similar format to the mutations file, but with each run’s mutations separated with ---

    Code Block
    --- position original_residue mutation 5 K S 42 T I --- position original_residue mutation 5 K S 42 T K ---

• --all-mutations

  • you can omit an input mutations-file and instead run in all-mutations mode, where all mutations at each position will be selected

• --dump-pdb

  • run with this flag to output the PDB for each mutation as well as the score

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