How to Create a Resfile

Design and Deimmunizer will sample mutations in a protein based on the instructions defined in a resfile. The file will be included when the design job is submitted with this flag.

--res-file=input.res

Example: design1.res

NATAA #Header provides instructions for all positions not specified in body. This header will allow and repack the native amino acids

START #Everything below this line is the body of the file and above this is considered the header

6 - 11 A ALLAA #For residue positions 6 to 11 in Chain A, allow all canonical amino acids to be sampled
24 A POLAR #Position 24 allowed to sample 9 polar residues only

File Structure

  • Resfile should have .res file type
  • A resfile consists of two main sections:
    • Header (optional): Specifies default commands that apply to all residues unless overridden.
    • Body (required): Specifies commands for individual residues, ranges of residues, or entire chains.
  • The body must start with the word START followed by residue-specific information.

Resfile Header

  • Contains default commands that apply globally to residues not explicitly defined in the body.
  • Commands are written as one or more lines, each ending with a newline (\n).

Resfile Body

  • Begins with the word START and defines residue-specific instructions.

Identifying Design Positions

  • The body specifies residues using three formats:
    • Single Residue:
      • Format: <PDBNUM> <CHAIN>
      • Example: 10 A (residue 10 in chain A - this is case sensitive so A and a are not the same)
    • Range of Residues:
      • Format: <PDBNUM> - <PDBNUM> <CHAIN>
      • Example: 5 - 10 B (residues 5 to 10 in chain B).
    • Entire Chain:
      • Format: * <CHAIN>
      • Example: * C (all residues in chain C).

Residue Commands

  • Commands specify what Rosetta should do with the identified residues.
  • Examples of commands:
    • ALLAA: Allow all 20 canonical amino acids
    • ALLAAxc: Allow all 20 canonical amino acids except cysteine
    • PIKAA W: Restricts this position to tryptophan
      • Can replace W with any amino acid
      • A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, Y
    • POLAR: Allow all 9 polar canonical amino acids (DEHKNQRST)
    • APOLAR: Allow all 11 nonpolar canonical amino acids (ACFGILMPVWY)
    • NOTAA : Disallow all amino acids listed
      • A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, Y
      • No spaces or nonAA should be between AAs in list
    • PIKAA : Allow only amino acids listed
    • NATRO: Preserve the input rotamer without repacking
    • NATAA: Allow and repack the native amino acid

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