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 T0280.a2m 
 NameTarget T0280
// 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 T0280.try5-opt2.pdb
ReadConformPDB T0280.try4-opt2.repack-nonPC.pdb
ReadConformPDB T0280.try1-opt2.pdb

InFilePrefix 
ReadConformPDB T0280.t2k.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
# ReadConformPDB T0280.t2k.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
# ReadConformPDB T0280.t2k.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
# ReadConformPDB T0280.t2k.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
# ReadConformPDB T0280.t2k.undertaker-align.pdb model 5
# PrintConformSheets align5.sheets
# PrintConformHelices align5.helices
# 
# ReadConformPDB T0280.t2k.undertaker-align.pdb model 6
# PrintConformSheets align6.sheets
# PrintConformHelices align6.helices
# 
# ReadConformPDB T0280.t2k.undertaker-align.pdb model 7
# PrintConformSheets align7.sheets
# PrintConformHelices align7.helices
# 
# ReadConformPDB T0280.t2k.undertaker-align.pdb model 8
# PrintConformSheets align8.sheets
# PrintConformHelices align8.helices
# 
# ReadConformPDB T0280.t2k.undertaker-align.pdb model 9
# PrintConformSheets align9.sheets
# PrintConformHelices align9.helices
# 
ReadConformPDB T0280.t2k.undertaker-align.pdb model 10
# PrintConformSheets align10.sheets
# PrintConformHelices align10.helices

# ReadConformPDB T0280.t2k.undertaker-align.pdb model 11
# PrintConformSheets align11.sheets
# PrintConformHelices align11.helices

# ReadConformPDB T0280.t2k.undertaker-align.pdb model 12
# PrintConformSheets align12.sheets
# PrintConformHelices align12.helices

# ReadConformPDB T0280.t2k.undertaker-align.pdb model 13
# PrintConformSheets align13.sheets
# PrintConformHelices align13.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