SetSeed

InfilePrefix 
// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
ReadTrainingAtoms dunbrack-2191.atoms
ReadRotamerLibrary dunbrack-2191.rot

InFilePrefix /projects/compbio/experiments/undertaker/spots/
    ReadAtomType exp-pdb.types
    ReadClashTable exp-pdb-2191-2symm.clash
    SetClashDefinition exp-pdb-2191-2symm

Time


//Need to read in target before specific fragments or alignments can
// be read, also before constraints can be defined.

InFilePrefix decoys/

ReadTargetPDB T0375.try9-opt2.pdb
NameTarget T0375

MakeGenericFragmentLibrary
Time


InFilePrefix 

Time

# If multimer is not already in pdb, but needs crystal symmetries to generate,
# then fetch the "biological unit" from pdb and use the following commands:

InFilePrefix 1vi9A/
ReadTemplatePDB 1vi9.pdb chain A name 1vi9A
ReadTemplatePDB 1vi9.pdb chain B name 1vi9B
ReadTemplatePDB 1vi9.pdb chain C name 1vi9C
ReadTemplatePDB 1vi9.pdb chain D name 1vi9D

ReadFragmentAlignment NOFILTER T0375-1vi9.4mer-a2m
OutFilePrefix 4mer/decoys/
PrintMultimerPDB 4 T0375.try9-opt2.4mer-1vi9.pdb
Time