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/T0328.try2-opt2.pdb
NameTarget T0328

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:
InFilePrefix 2gvkA/
ReadTemplatePDB 2gvk.mmol model 1 chain A name 2gvkA
ReadTemplatePDB 2gvk.mmol model 1 chain B name 2gvkB
ReadTemplatePDB 2gvk.mmol model 1 chain C name 2gvkC
ReadTemplatePDB 2gvk.mmol model 1 chain D name 2gvkD
ReadTemplatePDB 2gvk.mmol model 1 chain E name 2gvkE
ReadTemplatePDB 2gvk.mmol model 1 chain F name 2gvkF

OutFilePrefix 6mer/decoys/

InFilePrefix 2gvkA/
ReadFragmentAlignment NOFILTER T0328-2gvkA.6mer-a2m
InFilePrefix
PrintMultimerPDB 6 6mer-2gvkA-from-try2.pdb
Time