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 chimera-N1-C1.pdb
NameTarget T0472

MakeGenericFragmentLibrary
Time


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 3bid.pdb1 model 1 name 3bidA
// ReadTemplatePDB 3bid.pdb1 model 2 name 3bidB
# Or use the PQS mmol file
// ReadTemplatePDB 3bid.mmol chain A name 3bidA
// ReadTemplatePDB 3bid.mmol chain B name 3bidB

# OutFilePrefix decoys/
OutFilePrefix 

InFilePrefix 3bidA/
ReadFragmentAlignment NOFILTER T0472-3bidAB.a2m
InFilePrefix
PrintMultimerPDB 2 for-chimera-N1-C1-3bid.pdb
Time