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-1332.rot


InFilePrefix /projects/compbio/experiments/undertaker/spots/
#    ReadAtomType pdb-name.types
#    ReadClashTable pdb-1332-2symm.clash
#    SetClashDefinition pdb-2symm
    ReadAtomType exp-pdb.types
    ReadClashTable exp-pdb-1332-2symm.clash
    SetClashDefinition exp-pdb-2symm

Time


//Need to read in target before specific fragments or alignments can
// be read, also before constraints can be defined.

InFilePrefix 

 ReadTargetSeq T0248.a2m 
 NameTarget T0248
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

// include best previously found decoys!
InFilePrefix decoys/
OutfilePrefix decoys/
// include read-pdb.under

ReadConformPDB robetta-model2.pdb.gz    #3 domains, our fave
PrintConformSheets robetta-model2.sheets
PrintConformHelices robetta-model2.helices

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

ReadConformPDB robetta-model6.pdb.gz   
PrintConformSheets robetta-model6.sheets
PrintConformHelices robetta-model6.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