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

MakeGenericFragmentLibrary
Time

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

InFilePrefix ../decoys/
ReadTargetPDB T0440.try4-opt3.pdb
NameTarget T0440

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 1xxx.pdb1 model 1 name 1xxxA
// ReadTemplatePDB 1xxx.pdb1 model 2 name 1xxxB
# Or use the PQS mmol file
// ReadTemplatePDB 1xxx.mmol chain A name 1xxxA
// ReadTemplatePDB 1xxx.mmol chain B name 1xxxB

OutFilePrefix decoys/

InFilePrefix ../2yxoA/
ReadFragmentAlignment NOFILTER T0440-2yxoA.dimer-a2m
InFilePrefix
PrintMultimerPDB 2 dimer-try4-2yxo.pdb
Time


InFilePrefix ../decoys/
ReadTargetPDB T0440.try5-opt3.pdb
NameTarget T0440
Time

OutFilePrefix decoys/

InFilePrefix ../2yxoA/
ReadFragmentAlignment NOFILTER T0440-2yxoA.dimer-a2m
InFilePrefix
PrintMultimerPDB 2 dimer-try5-2yxo.pdb
Time