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 T0344.a2m 1
 NameTarget T0344
// 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
ReadConformPDB robetta-model1.pdb
PrintConformSheets robetta1.sheets
PrintConformHelices robetta1.helices

ReadConformPDB robetta-model2.pdb
PrintConformSheets robetta2.sheets
PrintConformHelices robetta2.helices

ReadConformPDB robetta-model3.pdb
PrintConformSheets robetta3.sheets
PrintConformHelices robetta3.helices

ReadConformPDB robetta-model4.pdb
PrintConformSheets robetta4.sheets
PrintConformHelices robetta4.helices

ReadConformPDB robetta-model5.pdb
PrintConformSheets robetta5.sheets
PrintConformHelices robetta5.helices

ReadConformPDB robetta-model6.pdb
PrintConformSheets robetta6.sheets
PrintConformHelices robetta6.helices

ReadConformPDB robetta-model7.pdb
PrintConformSheets robetta7.sheets
PrintConformHelices robetta7.helices

ReadConformPDB robetta-model8.pdb
PrintConformSheets robetta8.sheets
PrintConformHelices robetta8.helices

ReadConformPDB robetta-model9.pdb
PrintConformSheets robetta9.sheets
PrintConformHelices robetta9.helices

ReadConformPDB robetta-model10.pdb
PrintConformSheets robetta10.sheets
PrintConformHelices robetta10.helices


#adding in optimized robetta models

ReadConformPDB T0344.try5-opt2.pdb.gz
PrintConformSheets T0344.try5-opt2.sheets
PrintConformHelices T0344.try5-opt2.helices

ReadConformPDB T0344.try6-opt2.pdb.gz
PrintConformSheets T0344.try6-opt2.sheets
PrintConformHelices T0344.try6-opt2.helices

ReadConformPDB T0344.try7-opt2.pdb.gz
PrintConformSheets T0344.try7-opt2.sheets
PrintConformHelices T0344.try7-opt2.helices

ReadConformPDB T0344.try8-opt2.pdb.gz
PrintConformSheets T0344.try8-opt2.sheets
PrintConformHelices T0344.try8-opt2.helices

ReadConformPDB T0344.try9-opt2.pdb.gz
PrintConformSheets T0344.try9-opt2.sheets
PrintConformHelices T0344.try9-opt2.helices

ReadConformPDB T0344.try10-opt2.pdb.gz
PrintConformSheets T0344.try10-opt2.sheets
PrintConformHelices T0344.try10-opt2.helices

ReadConformPDB T0344.try11-opt2.pdb.gz
PrintConformSheets T0344.try11-opt2.sheets
PrintConformHelices T0344.try11-opt2.helices

ReadConformPDB T0344.try12-opt2.pdb.gz
PrintConformSheets T0344.try12-opt2.sheets
PrintConformHelices T0344.try12-opt2.helices

ReadConformPDB T0344.try13-opt2.pdb.gz
PrintConformSheets T0344.try13-opt2.sheets
PrintConformHelices T0344.try13-opt2.helices

ReadConformPDB T0344.try14-opt2.pdb.gz
PrintConformSheets T0344.try14-opt2.sheets
PrintConformHelices T0344.try14-opt2.helices

Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB opt-robetta-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