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 TR454.a2m 5
 NameTarget TR454
// 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 dimer/decoys/
ReadConformPDB TR454.try17-opt3.unpack.pdb chain A # < try13-opt3 < try12-opt3 < try10-opt3.unpack.gromacs0 < try7-opt3 < try4-opt3 < dimer-TR454.try3-2uxu < try2-opt3.gromacs0.repack-nonPC
# ReadConformPDB TR454.try13-opt3.unpack.pdb chain A # < try12-opt3 < try10-opt3.unpack.gromacs0 < try7-opt3 < try4-opt3 < dimer-TR454.try3-2uxu < try2-opt3.gromacs0.repack-nonPC
# ReadConformPDB TR454.try12-opt3.unpack.pdb chain A # < try10-opt3.unpack.gromacs0 < try7-opt3 < try4-opt3 < dimer-TR454.try3-2uxu < try2-opt3.gromacs0.repack-nonPC
ReadConformPDB TR454.try11-opt3.unpack.pdb chain A # < try10-opt3.unpack.gromacs0 < try7-opt3 < try4-opt3 < dimer-TR454.try3-2uxu < try2-opt3.gromacs0.repack-nonPC
# ReadConformPDB TR454.try10-opt3.unpack.pdb chain A # < try7-opt3 < try4-opt3 < dimer-TR454.try3-2uxu < try2-opt3.gromacs0.repack-nonPC
ReadConformPDB TR454.try10-opt3.unpack.gromacs0.repack-nonPC.pdb chain A # < try4-opt3 < dimer-TR454.try3-2uxu < try2-opt3.gromacs0.repack-nonPC
	# best rosetta energy

# ReadConformPDB TR454.try7-opt3.unpack.pdb chain A # < try4-opt3 < dimer-TR454.try3-2uxu < try2-opt3.gromacs0.repack-nonPC


# ReadConformPDB TR454.try4-opt3.unpack.pdb chain A # < dimer-TR454.try3-2uxu < try2-opt3.gromacs0.repack-nonPC

InFilePrefix decoys/
# ReadConformPDB TR454.try3-opt3.pdb # < try2-opt3.gromacs0.repack-nonPC
# ReadConformPDB TR454.try2-opt3.gromacs0.repack-nonPC.pdb # < TR454

InFilePrefix dimer/decoys/
ReadConformPDB TR454.try16-opt3.unpack.pdb chain A # < try15-opt3 < dimer-TR454.try14-2uxu
# ReadConformPDB TR454.try15-opt3.unpack.pdb chain A # < dimer-TR454.try14-2uxu
InFilePrefix decoys/
#  ReadConformPDB TR454.try14-opt3.pdb # < chimera-try9-try12

InFilePrefix dimer/decoys/
# ReadConformPDB TR454.try9-opt3.unpack.pdb chain A # < try8-opt3 < dimer-TR454.try6-2uxu
# ReadConformPDB TR454.try8-opt3.unpack.pdb chain A # < dimer-TR454.try6-2uxu
InFilePrefix decoys/
# ReadConformPDB TR454.try6-opt3.pdb # < chimera-try5-try4
# ReadConformPDB TR454.try5-opt3.pdb # < chimera-try3-try1


InFilePrefix dimer/decoys/
ReadConformPDB TR454.try19-opt3.unpack.pdb chain A # < dimer-TR454.try18-2uxu
InFilePrefix decoys/
# ReadConformPDB TR454.try18-opt3.pdb # < try1-opt3.repack-nonPC
# ReadConformPDB TR454.try1-opt3.pdb


# ReadConformPDB TR454.pdb
# PrintConformSheets init.sheets
# PrintConformHelices init.helices


InFilePrefix 
// ReadConformPDB TR454.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB TR454.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB TR454.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB TR454.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB TR454.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