SetSeed

InfilePrefix 
// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/
ReadTrainingAtoms monomeric-50pc.atoms
ReadRotamerLibrary dunbrack-1332.rot

InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/spots/
    ReadAtomType pdb-name.types
    ReadClashTable pdb-atom-name.clash
    SetClashDefinition pdb-atom-name

Time


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

# InFilePrefix 
# ReadTargetPDB dimer-1ihr-from_align.pdb
# PrintConformSheets dimer-1ihr-from_align.sheets
# PrintConformHelices align3.helices
Time

InfilePrefix decoys/
OutfilePrefix decoys/
ReadTargetPDB merged_dimer_from_align.pdb
NameTarget T0240
# PrintConformSheets merged_dimer_from_align.sheets
# PrintConformHelices merged_dimer_from_align.helices

# ReadConformPDB merged_dimer_from_try8.pdb
# PrintConformSheets merged_dimer_from_try8.sheets
# PrintConformHelices merged_dimer_from_try8.helices

ReadConformPDB merged_dimer_from_try9.pdb
PrintConformSheets merged_dimer_from_try9.sheets
PrintConformHelices merged_dimer_from_try9.helices

Time