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 T0393.try1-init.pdb
NameTarget T0393

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 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 chian B name 1xxxB

OutFilePrefix decoys/

InFilePrefix ../2izzA/
ReadFragmentAlignment NOFILTER T0393-2izzA.dimer-a2m
InFilePrefix
PrintMultimerPDB 2 symmetrize dimer-try1-init-2izz.pdb 
Time

ReadConformPDB ../decoys/T0393.try1-opt3.pdb
PrintMultimerPDB  2  symmetrize  dimer-try1-opt3-2izz.pdb
Time