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 T0342.a2m 1
 NameTarget T0342
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/


# put believed-to-be-best decoy first
# InFilePrefix decoys/
# ReadConformPDB chimera-22-shifted.pdb

InFilePrefix decoys/
ReadConformPDB T0342.try40-opt2.pdb


InFilePrefix K140-L188/decoys/
ReadConformPDB T0342.try2-opt2.pdb

Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB try40-opt2+K140-L188-try2-2.pdb superpose \
	atom K140.CB atom K141.CB atom I142.CB \
	atom I143.CB atom C144.CB atom M145.CA atom G146.CB \
	atom A147.CB atom K148.CB


Time

quit