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 T0368.a2m 1
 NameTarget T0368
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

InFilePrefix decoys/
# put believed-to-be-best decoy first
ReadConformPDB T0368.try34-opt2.pdb			# best try35.costfcn
ReadConformPDB T0368.try35-opt2.gromacs0.repack-nonPC.pdb # best robetta
ReadConformPDB T0368.try31-opt2.gromacs0.pdb		# best gromacs with try35.costfcn (not try34 or try35)
ReadConformPDB T0368.try33-opt2.repack-nonPC.pdb	# best rosetta without gromacs (not try35)
ReadConformPDB T0368.try32-opt2.pdb			# other decent choice



InFilePrefix decoys/
# ReadConformPDB tr368.pdb


Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB refine-models.pdb superpose \
	atom E74.CB atom A75.CB atom L76.CB \
	atom A79.CB atom D80.CB atom A82.CB atom L83.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