<header> start <body>
Throughout, the resfile has the following convetions:
#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)
<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!
- 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
- 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
- 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 )
- 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
1.5.2