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 T0306.a2m 1
 NameTarget T0306
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/
// include read-pdb.under

# put believed-to-be-best decoy first
InFilePrefix decoys/

# choose one of try20 or try5
ReadConformPDB T0306.try20-opt2.pdb
# ReadConformPDB T0306.try5-opt2.pdb

# choose one of try13 or try19 
# ReadConformPDB T0306.try19-opt2.pdb
ReadConformPDB T0306.try13-opt2.pdb


ReadConformPDB T0306.try23-opt2.pdb # from ProteinShop

ReadConformPDB T0306.try27-opt2.pdb	# from RAPTOR-ACE_TS1
ReadConformPDB T0306.try26-opt2.pdb	# from SPARKS_TS1


# really poor secondary match, but Rosetta likes it.
# ReadConformPDB T0306.try25-opt2.gromacs0.repack-nonPC.pdb

# ReadConformPDB T0306.try22-opt2.pdb
# ReadConformPDB T0306.try21-opt2.pdb

# ReadConformPDB T0306.try10-opt2.pdb
 
InFilePrefix 6mer/decoys/
# ReadConformPDB T0306.try3-opt2.unpack.pdb chain A
# ReadConformPDB T0306.try4-opt2.unpack.gromacs0.repack-nonPC.pdb chain A

InFilePrefix decoys/
# ReadConformPDB T0306.try4-opt2.pdb
# ReadConformPDB T0306.try1-opt2.pdb


InFilePrefix 
# ReadConformPDB T0306.undertaker-align.pdb model 1
# ReadConformPDB T0306.undertaker-align.pdb model 2
# ReadConformPDB T0306.undertaker-align.pdb model 3
# ReadConformPDB T0306.undertaker-align.pdb model 4
# ReadConformPDB T0306.undertaker-align.pdb model 5
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