Rosetta 3.1 Release Manual

Resfile syntax

This page describes the resfile format and syntax. The resfile contains information which is This file specifies which residues will be varied.

Features

There are few features of Rosetta Resfile:

Syntax and Semantics

The outline of a resfile is
<header>

start

<body>

Throughout, the resfile has the following convetions:

Header

Specify in the <header> section the commands that should be applied to all residues by default if no other commands are specified in the body. Commands in this section are NOT applied to any residue which has a line in the body section. You will NOT get extra rotamers at all positions if you put EX 1 in the header - it needs to be on the command line to apply to all positions, or repeated on all specified lines. For example
#For all residue positions that are not specified below:
ALLAA           # allow all amino acids
EX 1 EX 2       # allow extra chi rotameters at chi-id 1 and 2
USE_INPUT_SC    # allow the use of the input side chain conformation   ( see below for more detailed description of commands)

Body

Specify in the <body> section residue level information to be sent to the packer. Each line should have the following format,
<res-id> <one or more commands>

The <res-id> should be of the form <PDB residue="" id>=""> <chain>. If the pose you are working with has a blank chain in the PDB, put "_" in for the chain. For example:

10 _ PIKAA W  # Allow only Trp at residue 10 in the unlabeled chain
12 B NOTAA W # Disallow Trp at residue 12 in the B chain
0 A NOTAA W   # ERROR: residue 0 is not allowed!

Command Lines and Options

Commands for controlling sequence identity

Each command acts to restrict the allowed amino acids. If multiple commands are combined, only amino acids that are allowed by each command individually are included.
- ALLAAwc .............. allow all 20 amino acids ( default )
- ALLAAxc .............. allow all amino acids except cysteine
- POLAR ................ allow only canonical polar amino acids
- APOLAR ............... allow only canonical non polar amino acids
- NOTAA <list of AAs> .. disallow only the specified amino acids ( use one letter codes )
- PIKAA <list of AAs> .. allow only the specified amino acids ( use one letter codes )
- NATAA ................ allow only the native amino acid
- EMPTY ................ disallow all canonical amino acids ( for use with non canonicals )
- NC <ResidueTypeName> . allow a specific (non canonical) residue type, must be repeated for each type

Commands for controlling conformational freedom:

- NATRO  ...................................... fix natural rotamer ( fix identity and conformation )
- EX (ARO) <chi-id> ( LEVEL <sample level> ) .. ( see below for detailed description
- EX_CUTOFF <cutoff-level>  ................... about how to specify EX commands )
- USE_INPUT_SC ................................ include native rotamer

Commands for controlling the packer:

- AUTO  ......... add the behavior 'AUTO'
- SCAN  ......... add the behavior 'SCAN'
- NO_ADDUCTS .... disallow DNA adducts
- TARGET <AA> ... specify target amino acid ( use one letter codes )

Extra Chi commands

Extra chi commands control the degrees of freedom for the chi angles in the side chains.
- The <chi-id> specifies the PARTICULAR chi angle the command applied ( only numbers 1-4 are allowed )
- The ARO flag restricts the effects of the command to aromatic side chains.  Since aromatic side chains have at most 2 chi angles, <chi-id> must be '1' or '2'
- The LEVEL <sample-level> specifies how many extra chi angles to sample for each allowed rotamer:
   - 0 ...... no extra chi angles
   - 1 ...... sample at 1 standard deviation
   - 2 ...... sample at 1/2 standard deviation
 	 - 3 ...... sample at two full standard deviations
	 - 4 ...... sample at two 1/2 standard deviations
	 - 5 ...... sample at four 1/2 standard deviations
	 - 6 ...... sample at three 1/3 standard deviations
	 - 7 ...... sample at six 1/4 standard deviations
- The EX_CUTOFF command limits the number of extra chi sampled rotamers to include ( only numbers <18 with 18 begin default allowed ). Residues with more neighbors than <integer> will use the specified ex flags (i.e. ex1 etc.).  The default value 18 makes it so that only buried residues get the extra rotamers.  ex_cutoff 1 means all the residues get extra rotamers.

Here are some examples:

10 B  EX 1 EX 2
9  B  EX 3      # WARNING: probably want to include EX 1 and EX 2 if EX 3 is specified!
8  B  EX ARO 2
7  B  EX ARO 3 # ERROR: ARO only works for chi ids 1 and 2
6  B  EX 1 LEVEL 7

This resfile will provide packability at most locations, fixed rotamers at a few, and designability at a few. Note the liberal use of comments for clarity. NOTAA C is equivalent to ALLAAxc.

NATAA
start
#anchor
81      B       NATAA   #anchor
82      B       NATAA   #anchor
83      B       NATRO   #anchor
84      B       NATRO   #anchor
85      B       NATRO   #anchor
86      B       NATRO   #anchor

#loops

#133    B       NOTAA C #loop
134     B       NOTAA C #loop
135     B       NOTAA C #loop
136     B       NOTAA C #loop
137     B       NOTAA C #loop
138     B       NOTAA C #loop
139     B       NOTAA C #loop
140     B       NOTAA C #loop
141     B       NOTAA C #loop
142     B       NOTAA C #loop
#143    B       NOTAA C #loop
#144    B       NOTAA C #loop
#145    B       NOTAA C #loop

#77     B       NOTAA C #loop
#78     B       NOTAA C #loop
#79     B       NOTAA C #loop
80      B       NOTAA C #loop
#ANCHOR
87      B       NOTAA C #loop
88      B       NOTAA C #loop
#89     B       NOTAA C #loop

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