mods

Specifies modifications to the sequence or structure in the PDB file

Single-valued attributes:

• mutations: Single-residue mutations, expressed as shortcodes (e.g., C:F32A to mutate residue 32 of chain C from PHE to ALA); note that the residue must be present in the PDB source file, and that the mutation will not be made if the residue is not present

  Example:

  mutations:
  - C:F32A
  - A:TRP,100,ARG
  - B:K50M
  

• ssbonds: additional ssbonds, expressed as shortcodes; e.g., C_154-A_298 to add an ssbond between resids 154 of chain C and 298 of chain A. Note that the indicated residues must by CYS’s. If they are not, you should include each in a mutation shortcode in the mutations list

  Example:

  ssbonds:
  - C_154-A_298
  - A_100-B_200
  

• ssbondsdelete: existing ssbonds to break, expressed as shortcodes; e.g., C_154-A_298 will break the existing ssbond between resids 154 of chain C and 298 of chain A so that each is a reduced CYS.

  Example:

  ssbondsdelete:
  - C_154-A_298
  - A_100-B_200
  

• links: additional generic bonds, expressed as shortcodes; e.g., C_154_N-A_298_M to add a link between atom N of resid 154 of chain C and atom M of resid 298 of chain A.

  Example:

  links:
  - C_154_N-A_298_M
  - A_100_CA-B_200_O
  

• deletions: residue ranges to delete, expressed as shortcodes; e.g., C:99-101 deletes residues 99 to 101 (inclusive) of chain C

  Example:

  deletions:
  - C:99-101
  - A:50-60
  

• substitutions: residue ranges to replace with a new sequence; e.g., C:99-101,GG replaces residues 99, 100, and 101 of chain C with two glycines

  Example:

  substitutions:
  - C:99-101,GG
  - A:50-60,GGG
  

• insertions: sequence of residues to insert C-terminal to a specified residue in a specified chain; e.g., C,123,GRETA inserts the residues Gly123A, Arg123B, Glu123C, Thr123D, and Ala123E immediately C-terminal to residue 123 of chain C; if the resid includes a terminal “+”, then inserted resids are incremented as integers

  Example:

  insertions:
  - C,123,GRETA
  - A,50,GGG+
  

• patches: CHARMM36-style patches to apply to the system

  Example:

  patches:
  - ASPP:C:199
  

• crotations: dihedral angle rotations

  Example:

  crotations:
  - psi,E,661,693,60
  - phi,E,662,693,60
  - alpha,B,33,52
  - alpha,B,144,153
  - alpha,D,32,52
  - alpha,D,144,153
  

• transrot: global translations and rotations

• Cfusions: fuse residues from named residue range of named protein chain of named input PDB coordinate file to C-terminus of named segment of base molecule

• grafts: graft residues from named residue range of named chain of named input PDB coordinate file onto target residue of base molecule

  Example:

  grafts:
  - A_1304:4b7i,C_1-8
  - B_1304:4b7i,C_1-8
  - C_1304:4b7i,C_1-8
  - A_1305:4b7i,C_1-8
  - B_1305:4b7i,C_1-8
  - C_1305:4b7i,C_1-8
  

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