boltzgen/example/denovo_zinc_finger_against_dna/zinc_finger.yaml

entities:
  # Specification of the target which is extracted from a .cif file
  - file:
      path: zf.cif
      # Which parts of the .cif file to include as target (here includes all chains/residues)
      include: "all" 
      # Which parts of the included content to exclude (here excludes residues 10, 63..69, and 185.. in chain A1)
      exclude:
        - chain:
            id: A1
            res_index: ..10,63..69,185..
      # Where to insert new designable residues into existing chains
      # Here we insert 3..8 residues after residue 63 in chain A1
      design_insertions:
        - insertion:
            id: A1
            res_index: 63 
            num_residues: 3..8
      # Which regions of the target should have their structure specified
      # Here we hide everything (no structure specified)
      structure_groups:
        - group:
            visibility: 0
            id: "all"
      # Which residues in the target should be redesigned
      # Here we declare A1:11..184 to be redesigned
      design:
        - chain:
            id: A1
            res_index: 11..184
      # Which residues in the target are explicitly not redesignable (override entries in design)
      # Here we carve out fixed positions on chain A1 to not be redesigned
      not_design:
        - chain:
            id: A1
            res_index: 11..20,29,33,39..48,57,61,72..81,90,94,100..109,118,122,129..138,147,151,157..166,175,179
      # Reset residue numbering to be contiguous for chain A1
      reset_res_index:
        - chain:
            id: A1