SetSeed


// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
 InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
 ReadTrainingAtoms monomeric-50pc.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 

Time

InFilePrefix decoys/
ReadTargetPDB T0373.try1-opt2.pdb
 NameTarget T0373

Time

OutFilePrefix

InFilePrefix 2a61A/
ReadFragmentAlignment NOFILTER T0373-2a61A.split-a2m force_alignment
PrintMultimerPDB 2 for-chimera-1-2a61A.pdb

Time

quit