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 T0472.try12-opt3.unpack.pdb chain A
NameTarget T0472

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 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/

InFilePrefix ../3bidA/


ReadFragmentAlignment NOFILTER T0472-3bidAG-Cterm.dimer-a2m
PrintMultimerPDB 2 dimer-try12-AG-Cterm.pdb
Time


ReadFragmentAlignment NOFILTER T0472-3bidAG.dimer-a2m
PrintMultimerPDB 2 dimer-try12-AG.pdb
Time


InFilePrefix decoys/
ReadTemplatePDB T0472.try11-opt3.unpack.pdb chain A name A
ReadTemplatePDB T0472.try11-opt3.unpack.pdb chain B name B
ReadFragmentAlignment NOFILTER dimer-try11.a2m

PrintMultimerPDB 2 dimer-try12-from-try11.pdb