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 T0300.a2m 1
ReadTargetPDB decoys/T0300.try5-opt2.unpack.pdb		# use two-chain numbering
 NameTarget T0300
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

// include best previously found decoys!
InFilePrefix decoys/
OutfilePrefix decoys/
// include read-pdb.under

# put believed-to-be-best decoy first
ReadConformPDB T0300.try5-opt2.unpack.pdb
multimer 2
ReadConformPDB T0300.try4-opt2.unpack.pdb
multimer 2
ReadConformPDB T0300.try7-opt2.unpack.pdb
multimer 2
ReadConformPDB T0300.try8-opt2.unpack.pdb
multimer 2
ReadConformPDB T0300.try6-opt2.unpack.pdb
multimer 2


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