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 T0329.a2m 1
 NameTarget T0329
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time


InFilePrefix decoys/

# the best structure so far (polished from try10)
ReadConformPDB T0329.try14-opt2.pdb

# the best polished from from try8 from try4
ReadConformPDB T0329.try13-opt2.pdb


// polished try4
// ReadConformPDB T0329.try8-opt2.pdb


# the first decent structure
# and once rosetta's favorite (before try13 and try14)
ReadConformPDB T0329.try4-opt2.repack-nonPC.pdb


// ReadConformPDB T0329.try5-opt2.pdb



// # -A- model I'm currently trying to improve
// InFilePrefix chimera/
// ReadConformPDB chimera.pdb


InFilePrefix 

# -B- model (potential alternative structure)
 ReadConformPDB T0329.undertaker-align.pdb model 1	# from t04 2ah5A

# -B- model (potential alternative structure)
# ReadConformPDB T0329.undertaker-align.pdb model 2	# from t04 2gfhA

# elaborated -A- model (that my tries are based on)
ReadConformPDB T0329.undertaker-align.pdb model 5	# from t06 1swvA



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