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/T0308.try5-opt2.pdb.gz
NameTarget T0308

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 3mer/
ReadTemplatePDB  T0308.t9o2-t10o2-trimer.pdb chain A name 3merA
ReadTemplatePDB  T0308.t9o2-t10o2-trimer.pdb chain B name 3merB
ReadTemplatePDB  T0308.t9o2-t10o2-trimer.pdb chain C name 3merC

OutFilePrefix 3mer/decoys/

InFilePrefix 3mer/
ReadFragmentAlignment NOFILTER T0308-model.3mer-a2m
InFilePrefix
PrintMultimerPDB 3 3mer-try1-model.pdb
Time