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 TR454.try14-opt3.pdb
NameTarget TR454

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:
// ReadTemplatePDB 1p6b.pdb1 model 1 name 1p6bA
// ReadTemplatePDB 1p6b.pdb1 model 2 name 1p6bB
# Or use the PQS mmol file
// ReadTemplatePDB 1p6b.mmol chain A name 1p6bA
// ReadTemplatePDB 1p6b.mmol chain B name 1p6bB

OutFilePrefix decoys/

InFilePrefix ../1pb6A/
ReadFragmentAlignment NOFILTER TR454-1pb6A.dimer-a2m
InFilePrefix
PrintMultimerPDB 2 dimer-TR454.try14-1pb6.pdb
Time

InFilePrefix ../2uxuA/
ReadFragmentAlignment NOFILTER TR454-2uxuA.dimer-a2m
InFilePrefix
PrintMultimerPDB 2 dimer-TR454.try14-2uxu.pdb
Time