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-2191.rot


InFilePrefix /projects/compbio/experiments/undertaker/spots/
    ReadAtomType exp-pdb.types
    ReadClashTable exp-pdb-2191-2symm.clash
    SetClashDefinition exp-pdb-2191-2symm

Time


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

InFilePrefix 

 ReadTargetSeq T0342.a2m 1
 NameTarget T0342
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/


# put believed-to-be-best decoy first
InFilePrefix decoys/
ReadConformPDB T0342.try56-opt2.pdb
ReadConformPDB T0342.try55-opt2.gromacs0.repack-nonPC.pdb
ReadConformPDB T0342.try52-opt2.pdb

#ReadConformPDB ProteinShop/try36-shifted.pdb 

//not sure of which of the following models to submit for the fifth choice.
#  ReadConformPDB T0342.try22-opt2.gromacs0.repack-nonPC.pdb
# ReadConformPDB T0342.try46-opt2.pdb
ReadConformPDB T0342.try40-opt2.pdb

# ReadConformPDB T0342.try53-opt2.pdb
# ReadConformPDB T0342.try19-opt2.pdb
# ReadConformPDB T0342.try9-opt2.pdb
ReadConformPDB T0342.try16-opt2.pdb


InFilePrefix 
# ReadConformPDB T0342.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
#  PrintConformHelices align1.helices
#ReadConformPDB T0342.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
#ReadConformPDB T0342.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
#ReadConformPDB T0342.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
#ReadConformPDB T0342.undertaker-align.pdb model 5
# PrintConformSheets align5.sheets
# PrintConformHelices align5.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	...
atom K140.CA1	K141.CA

Time

quit