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 durnbrack-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/T0380.try3-opt2.pdb.gz
NameTarget T0380

MakeGenericFragmentLibrary
Time

^L
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 2fhq.pdb1 model 1 name 2fhqA  
//ReadTemplatePDB 2fhq.pdb1 model 2 name 2fhqB

OutFilePrefix dimer/decoys/

InFilePrefix 2fhqA/
ReadFragmentAlignment NOFILTER 2fhqA.dimer-a2m
InFilePrefix
PrintMultmierPDB 2 dimer-2fhqA-from-try3-opt2.pdb
Time