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 dimer/decoys/
ReadTargetPDB T0327.try11-opt2.unpack.pdb chain A
NameTarget T0327

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 1ub9A/1ub9.pdb1 chain A name 1ub9A
ReadTemplatePDB 1ub9A/1ub9.pdb1 chain B name 1ub9B

OutFilePrefix dimer/decoys/

InFilePrefix 1ub9A/
ReadFragmentAlignment NOFILTER force_alignment T0327-1ub9A.dimer-a2m
PrintMultimerPDB 2 dimer-1ub9A-dimer11.pdb