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 TR435.a2m 15
 NameTarget TR435
// 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 TR435.try7-opt3.pdb # < from-GOOF-try5 < try3-opt3.gromacs0 < try2-opt3 < TR435
ReadConformPDB TR435.try8-opt3.pdb # < from-GOOF-try6 < try4-opt3.gromacs0 < try1-opt3 < align(2qpwA)

ReadConformPDB TR435.try7-opt3.gromacs0.repack-nonPC.pdb # < from-GOOF-try5 < try3-opt3.gromacs0 < try2-opt3 < TR435

ReadConformPDB TR435.try1-opt3.gromacs0.repack-nonPC.pdb # < align(1ku3A)


# InFilePrefix GOOF/decoys/
# ReadConformPDB TR435.try5-opt3.pdb  # < try3-opt3.gromacs0 < try2-opt3 < TR435
#  PrintConformSheets try5.sheets
#  PrintConformHelices try5.helices
# ReadConformPDB TR435.try6-opt3.pdb  # < try4-opt3.gromacs0 < try1-opt3 < align(2qpwA)
#  PrintConformSheets try6.sheets
#  PrintConformHelices try6.helices


InFilePrefix decoys/
# ReadConformPDB TR435.pdb
#  PrintConformSheets init.sheets
#  PrintConformHelices init.helices

InFilePrefix 
// ReadConformPDB TR435.undertaker-align.pdb model 1
 PrintConformSheets align1.sheets
 PrintConformHelices align1.helices
// ReadConformPDB TR435.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB TR435.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB TR435.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB TR435.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	...

Time

quit