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Predict 1000 new sequences for an input PDB using an elevated temperature (default temperature is 0.1

cyrus engine submit protein-mpnn 1ubq.pdb --n-mpnn-designs 1000 --sampling-temperature 0.2

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• --pdb-file

  • The path to a PDB file containing the protein backbone you want to design sequences for

• --n-mpnn-designs

  • The number of sequences to design, default is 1

• --sampling-temperature

  • The sampling temperature of the model, default is 0.1, higher values will result in more variation of output sequenes

• --gpu-type

  • The GPU to run the model on, default is t4. Set this to a100 if you are generating a very large number of sequences

• --fixed-residue-positions

  • A space separated list of fixed residue positions following the format. i.e. ‘A1-10 A12 A15 B1-10'

    Individual positions: <Chain><Start>
    Ex: 'A1 A2 A3 A4'
    Subsequent positions: <Chain><Start>-<End>
    Ex: ‘A1-4’

• --symmetric-chains

  • Chains which should be treated symmetrically having their sequences matched at each position. They are defined in space separated sets with each chain in the set separated by a -. A tetramer composed of two unique homodimers would be defined as “A-B Y-Z”

• --tied-positions

  • Residues which should be symmetrically tied together such that mutating one automatically mutates the other. They are defined in sets separated by a space with each element chain separated by a slash and positions in the set being separated by a dash . i.e. “A1-10/B1-10 C5-10/D5-10”

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