Resfile.format

This file specifies which residues will be varied during the design run.
Below is an example resfile which performs design at a subset of positions and repacking everywhere else. Fields are whitespace delimited.

NATAA
EX 1
USE_INPUT_SC

start
6 A ALLAAwc EX 1 EX 2
21 A ALLAA EX 1 EX 2
29 A PIKAA DEKR EX 1 EX 2 EX 3
16 A POLAR EX 1 EX 2
18 A NATRO

The fields are as follows:
residue_number (whitespace) chain (whitespace) command

The available commands are as follows:
NATRO ............... fix natural rotamer ( fix identity and conformation )
ALLAAwc .............. allow all 20 amino acids ( default, same as ALLAA )
ALLAAxc .............. allow all amino acids except cysteine
POLAR ................ allow only canonical polar amino acids
APOLAR ............... allow only canonical non polar amino acids
NOTAA .. disallow only the specified amino acids ( use one letter codes )
PIKAA .. allow only the specified amino acids ( use one letter codes )
NATAA ................ allow only the native amino acid

EX (ARO) <chi-id> ( LEVEL <sample level> )
EX_CUTOFF <cutoff-level>
USE_INPUT_SC ................................ include native rotamer

For the full resfile format specification, see the Rosetta 3.5 Release Manual, Resfile Documentation