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 

ReadTargetPDB decoys/T0342.try16-opt2.pdb
NameTarget T0342

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


InFilePrefix 1v30A/
 ReadTemplatePDB 1v30.mmol chain A name 1v30A
 ReadTemplatePDB 1v30.mmol chain B name 1v30B

OutFilePrefix dimer/decoys/

InFilePrefix 1v30A/
ReadFragmentAlignment NOFILTER T0342-1v30A.dimer-a2m
InFilePrefix
PrintMultimerPDB 2 dimer-1v30-try16.pdb
Time