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 T0484.a2m 1
 NameTarget T0484
// 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/
// include read-pdb.under

# Pick ONE or TWO of these BAKER-ROBETTA_TS2 models
ReadConformPDB T0484.MQAY9-opt3.pdb	# < Pcons_dot_net_TS1 =? BAKER-ROBETTA_TS2
# ReadConformPDB T0484.try9-opt3.pdb	# < try8-opt3 < MQAU4-opt3 < Pcons_dot_net_TS1 =? BAKER-ROBETTA_TS2
# ReadConformPDB T0484.try8-opt3.pdb	# <  MQAU4-opt3 < Pcons_dot_net_TS1 =? BAKER-ROBETTA_TS2
# ReadConformPDB T0484.MQAU4-opt3.pdb	# < Pcons_dot_net_TS1 =? BAKER-ROBETTA_TS2
#  ReadConformPDB T0484.MQAC4-opt3.pdb	# < Pcons_dot_net_TS1 =? BAKER-ROBETTA_TS2
  # MQAC4 similar to MQAU4, but scores worse
ReadConformPDB T0484.MQAU4-opt3.gromacs0.repack-nonPC.pdb	# < Pcons_dot_net_TS1 =? BAKER-ROBETTA_TS2
	# best rosetta energy

# include this one with a rather different orientation??
# ReadConformPDB T0484.MQAY11-opt3.pdb	# < BAKER-ROBETTA_TS2
	# claims to be based on BAKER-ROBETTA_TS2, but rather different.
	# BAD BREAKS though.


# Pick TWO of these models based on 1o06A.
ReadConformPDB T0484.try11-opt3.pdb	# < try7-opt3 < try6-opt3 < align(1o06A?)
# ReadConformPDB T0484.try12-opt3.pdb	# < align(1o06A?)
# ReadConformPDB T0484.try7-opt3.pdb	# < try6-opt3 < align(1o06A?)
# ReadConformPDB T0484.try6-opt3.pdb	# < align(1o06A?)
# ReadConformPDB T0484.try5-opt3.pdb	# < align(1o06A?)
# ReadConformPDB T0484.try4-opt3.pdb	# < align(1o06A?)
ReadConformPDB T0484.try3-opt3.gromacs0.repack-nonPC.pdb	# < align(1o06A?)
	# best rosetta of the 1o06A models

# Pick one RBO-Proteus_TS4 model
ReadConformPDB T0484.MQAY4-opt3.pdb	# < RBO-Proteus_TS4
#  ReadConformPDB T0484.MQAY1-opt3.pdb	# < RBO-Proteus_TS4
  # MQAY1 similar to MQAY4, but scores worse



# Too awful to keep
# ReadConformPDB T0484.try2-opt3.pdb	# < try1-opt3 < align(1fusA?)
# ReadConformPDB T0484.try1-opt3.pdb	# < align(1fusA?)


InFilePrefix 
// ReadConformPDB T0484.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0484.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0484.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0484.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0484.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