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 T0272.a2m 
 NameTarget T0272
// 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

InFilePrefix 
ReadConformPDB T0272.t2k.undertaker-align.pdb model 1
PrintConformSheets align1.sheets
PrintConformHelices align1.helices
ReadConformPDB T0272.t2k.undertaker-align.pdb model 2
PrintConformSheets align2.sheets
PrintConformHelices align2.helices
ReadConformPDB T0272.t2k.undertaker-align.pdb model 3
PrintConformSheets align3.sheets
PrintConformHelices align3.helices
ReadConformPDB T0272.t2k.undertaker-align.pdb model 4
PrintConformSheets align4.sheets
PrintConformHelices align4.helices
ReadConformPDB T0272.t2k.undertaker-align.pdb model 5
PrintConformSheets align5.sheets
PrintConformHelices align5.helices
ReadConformPDB T0272.t2k.undertaker-align.pdb model 6
PrintConformSheets align6.sheets
PrintConformHelices align6.helices
ReadConformPDB T0272.t2k.undertaker-align.pdb model 7
PrintConformSheets align7.sheets
PrintConformHelices align7.helices
ReadConformPDB T0272.t2k.undertaker-align.pdb model 8
PrintConformSheets align8.sheets
PrintConformHelices align8.helices

Time

quit