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
AddId 1mkmA
AddId 1mkmB
AddId 2g7uA
AddId 2g7uB
ReadTrainingPDBIds


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 

ReadTargetPDB T0381.undertaker-align.pdb model 1
NameTarget T0381

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 1mkm.pdb1 model 1 name 1mkmA
// ReadTemplatePDB 1mkm.pdb1 model 2 name 1mkmB
# Or use the PQS mmol file
// ReadTemplatePDB 1mkm.mmol chain A name 1mkmA
// ReadTemplatePDB 1mkm.mmol chian B name 1mkmB

OutFilePrefix dimer/decoys/

InFilePrefix 1mkmA/
ReadFragmentAlignment NOFILTER T0381-1mkmA.dimer-a2m
InFilePrefix
PrintMultimerPDB 2 dimer-1mkmA-1mkm.pdb
Time


InFilePrefix 

ReadTargetPDB T0381.undertaker-align.pdb model 2
NameTarget T0381

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 2g7u.pdb1 model 1 name 2g7uA
// ReadTemplatePDB 2g7u.pdb1 model 2 name 2g7uB
# Or use the PQS mmol file
// ReadTemplatePDB 2g7u.mmol chain A name 2g7uA
// ReadTemplatePDB 2g7u.mmol chian B name 2g7uB

OutFilePrefix dimer/decoys/

InFilePrefix 2g7uA/
ReadFragmentAlignment NOFILTER T0381-2g7uA.dimer-a2m
InFilePrefix
PrintMultimerPDB 2 dimer-2g7uA-2g7u.pdb
Time