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 

 ReadTargetSeq T0347.a2m 1
 NameTarget T0347
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/


InFilePrefix decoys/
ReadConformPDB T0347.try1-opt2.pdb

InFilePrefix G95-E205/decoys/
ReadConformPDB T0347.try2-opt2.pdb
Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB for-chimera-1-2.pdb superpose \
	atom K96.CB atom D97.CB atom E98.CB atom F99.CB atom W100.CB \
	atom S106.CB atom V107.CB atom M108.CB atom D109.CB atom H110.CB

Time

quit