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 T0273.a2m 
 NameTarget T0273
// 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

# put believed-to-be-best decoy first
ReadConformPDB T0273.try1-opt2.pdb

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



InFilePrefix 
ReadConformPDB T0273.t2k.undertaker-align.pdb model 1
PrintConformSheets align1.sheets
PrintConformHelices align1.helices
ReadConformPDB T0273.t2k.undertaker-align.pdb model 2
PrintConformSheets align2.sheets
PrintConformHelices align2.helices
ReadConformPDB T0273.t2k.undertaker-align.pdb model 3
PrintConformSheets align3.sheets
PrintConformHelices align3.helices
ReadConformPDB T0273.t2k.undertaker-align.pdb model 4
PrintConformSheets align4.sheets
PrintConformHelices align4.helices
ReadConformPDB T0273.t2k.undertaker-align.pdb model 5
PrintConformSheets align5.sheets
PrintConformHelices align5.helices

Time


quit