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 T0331.a2m 1
 NameTarget T0331
// 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 dimer/decoys/
ReadConformPDB T0331.try7-opt2.unpack.pdb chain A
ReadConformPDB T0331.try9-opt2.unpack.pdb chain A
ReadConformPDB T0331.try8-opt2.unpack.pdb chain A

InFilePrefix 
ReadConformPDB T0331.undertaker-align.pdb model 1	# t2k alignment to 1g79A
# ReadConformPDB T0331.undertaker-align.pdb model 2
# ReadConformPDB T0331.undertaker-align.pdb model 3
# ReadConformPDB T0331.undertaker-align.pdb model 4
ReadConformPDB T0331.undertaker-align.pdb model 5	# t06 alignment 2fhqA

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 

# 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