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 T0322.a2m 1
 NameTarget T0322
// 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/
// include read-pdb.under
ReadConformPDB T0322.try3-opt2.pdb
ReadConformPDB T0322.try2-opt2.pdb
ReadConformPDB T0322.try9-opt2.pdb
ReadConformPDB T0322.try8-opt2.pdb
ReadConformPDB T0322.try1-opt2.pdb

Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB best-models.pdb superpose \
	atom N55.CB atom H61.CB atom G62.CA atom G63.CA atom D70.CB \
	atom T87.CB  atom F94.CB \
	atom G101.CA atom D102.CB atom V104.CB atom I124.CB

	

# Can specify a set of atoms as optional arguments of printAllConformPDB
# to give initial set of atoms to align.
# Format: 	atom A7.CA	atom K252.CA	...

Time

quit