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 T0354.a2m 1
 NameTarget T0354
// 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 decoys/
// include read-pdb.under

#try18 comes from a Proteinshop model that was based on try15 -> try10 -> try7
#try18 scores best with the try18 costfcn and scores 2nd using unconstrained
ReadConformPDB T0354.try18-opt2.pdb

#try15 comes from a Proteinshop model that was based on try10 -> try7
#try15 scores 2nd best using try18's costfcn and 3rd best using unconstrained
# try15-opt2.gromacs0.repack-nonPC is rosetta's favorite of the models
#it repacked.
ReadConformPDB T0354.try15-opt2.gromacs0.repack-nonPC.pdb

#try14 came from try10-opt2 which came from try7
#try14 scores 3rd best using try18's costfcn and 5th using unconstrained
ReadConformPDB T0354.try14-opt2.pdb

#try12 is the best scoring model using the unconstrained costfunction
#try12 is based on SAM_T06_server_TS1 and str2 constraints
ReadConformPDB T0354.try12-opt2.pdb

#try17 comes from a  Proteinshop model that was based on try7
#try17 doesn't score incredibly good, but is different enough I feel.
ReadConformPDB T0354.try17-opt2.pdb


InFilePrefix 
#ReadConformPDB T0354.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
#ReadConformPDB T0354.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
#ReadConformPDB T0354.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
#ReadConformPDB T0354.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
#ReadConformPDB T0354.undertaker-align.pdb model 5
#ReadConformPDB T0354.undertaker-align.pdb model 6
#ReadConformPDB T0354.undertaker-align.pdb model 7
#ReadConformPDB T0354.undertaker-align.pdb model 8
#ReadConformPDB T0354.undertaker-align.pdb model 9
# PrintConformSheets align5.sheets
# PrintConformHelices align5.helices

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