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 T0454.a2m 1
 NameTarget T0454
// 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 T0454.try7-opt3.unpack.pdb chain A	#< dimer-try6-1vi0 < try2-opt3

ReadConformPDB T0454.try5-opt3.unpack.pdb chain A	#< dimer-MQAU2-1pb6

# ReadConformPDB T0454.try4-opt3.unpack.gromacs0.pdb chain A	#< dimer-broken-1vi0 < dimer-try2-1vi0
ReadConformPDB T0454.try3-opt3.unpack.gromacs0.repack-nonPC.pdb #< dimer-try2-1vi0

InFilePrefix decoys/
ReadConformPDB T0454.MQAU2-opt3.pdb	# < MUProt_TS3
ReadConformPDB T0454.MQAC2-opt3.pdb	# < Phyre_de_novo_TS1

# ReadConformPDB T0454.try2-opt3.pdb	# < try1-opt3 < align(1vi0A)
# ReadConformPDB T0454.try1-opt3.gromacs0.pdb # < align(1vi0A)

InFilePrefix 
// ReadConformPDB T0454.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
//  ReadConformPDB T0454.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
# ReadConformPDB T0454.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0454.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0454.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