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 TR453.a2m 5
 NameTarget TR453
// 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 TR453.try6-opt3.gromacs0.repack-nonPC.pdb	# < chimera-V8-W15
	# best Rosetta energyy

ReadConformPDB TR453.try7-opt3.pdb	# < try5-opt3.gromacs0  < chimera-L32_I44
# ReadConformPDB TR453.try5-opt3.pdb	# < chimera-L32_I44

ReadConformPDB TR453.try8-opt3.pdb	# < try6-opt3.gromacs0  < chimera-V8-W15

# ReadConformPDB TR453.try3-opt3.pdb	# < try1-opt3.gromacs0 < align(2p13A)
# ReadConformPDB TR453.try1-opt3.pdb	# < align(2p13A)

ReadConformPDB TR453.try4-opt3.pdb	# < chimera-D76-D83

ReadConformPDB TR453.try2-opt3.pdb	# < TR453


# ReadConformPDB TR453.pdb
# PrintConformSheets init.sheets
# PrintConformHelices init.helices



InFilePrefix 
// ReadConformPDB TR453.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB TR453.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB TR453.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB TR453.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB TR453.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