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-try9-MQAU1.pdb
NameTarget T0413

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 2hu5.pdb1 model 1 name 2hu5A
// ReadTemplatePDB 2hu5.pdb1 model 2 name 2hu5B
# Or use the PQS mmol file
// ReadTemplatePDB 2hu5.mmol chain A name 2hu5A
// ReadTemplatePDB 2hu5.mmol chian B name 2hu5B

OutFilePrefix decoys/

ReadTemplatePDB decoys/T0413.try12-opt3.unpack.pdb chain A name try12A
ReadTemplatePDB decoys/T0413.try12-opt3.unpack.pdb chain B name try12B

InFilePrefix 
ReadFragmentAlignment NOFILTER dimer-try12.a2m


InFilePrefix
PrintMultimerPDB 2 dimer-chimera-try12.pdb
Time