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 T0476.a2m 1
 NameTarget T0476
// 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
ReadConformPDB T0476.try12-opt3.pdb     # < T0476.try8-opt3 < BAKER-ROBETTA_TS5  #best scoring with try12.costfcn 

ReadConformPDB T0476.try10-opt3.gromacs0.repack-nonPC.pdb    # <  T0476.try5-opt3 < try2-opt3 < MQAU1-opt3.gromacs0 < BAKER-ROBETTA_TS5
	# best Rosetta energy
# ReadConformPDB T0476.try5-opt3.gromacs0.repack-nonPC.pdb	# < try2-opt3 < MQAU1-opt3.gromacs0 < BAKER-ROBETTA_TS5
# ReadConformPDB T0476.try2-opt3.pdb	# < MQAU1-opt3.gromacs0 < BAKER-ROBETTA_TS5

ReadConformPDB T0476.try11-opt3.pdb     # < T0476.MQAY6-opt3 < BAKER-ROBETTA_TS2

# ReadConformPDB T0476.try9-opt3.pdb      # < T0476.try8-opt3 < BAKER-ROBETTA_TS5
# ReadConformPDB T0476.try8-opt3.pdb	# < MQAX6-try3 < BAKER-ROBETTA_TS5
# ReadConformPDB T0476.MQAX6-opt3.pdb	# < BAKER-ROBETTA_TS5


ReadConformPDB T0476.MQAY6-opt3.pdb	# < BAKER-ROBETTA_TS2

ReadConformPDB T0476.MQAY13-opt3.pdb	# < RBO-Proteus_TS1

# trying for disulfides:
# ReadConformPDB T0476.try4-opt3.pdb	# < try3-opt1 < MQAC1-opt3.repack-nonPC < BAKER-ROBETTA_TS5
# ReadConformPDB T0476.try3-opt3.pdb	# < MQAC1-opt3.repack-nonPC < BAKER-ROBETTA_TS5

#ReadConformPDB T0476.MQAC1-opt3.pdb	# < BAKER-ROBETTA_TS5
# ReadConformPDB T0476.MQAU1-opt3.pdb	# < BAKER-ROBETTA_TS5

#ReadConformPDB T0476.try1-opt3.pdb	# < align(2gx9A)


InFilePrefix 
// ReadConformPDB T0476.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0476.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0476.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0476.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0476.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 \
	residue C4	residue C7	residue C47 residue C50

# 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