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 T0482.a2m 1
 NameTarget T0482
// 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 T0482.try13-opt3.pdb	# < try12-opt3 < try10-opt3.pdb < chimera-try2-try7
# ReadConformPDB T0482.try12-opt3.pdb	# < try10-opt3.pdb < chimera-try2-try7
# ReadConformPDB T0482.try10-opt3.pdb	# < chimera-try2-try7
# ReadConformPDB T0482.try9-opt3.repack-nonPC.pdb	# < chimera-try2-try7

# ReadConformPDB T0482.try7-opt3.pdb	# < try4-opt3.gromacs0 < T0482.MQAX2-opt3 < Pcons_dot_net_TS4 =? BAKER_ROBETTA_TS1
# ReadConformPDB T0482.try4-opt3.pdb	# < MQAX2-opt3 < Pcons_dot_net_TS4 =? BAKER_ROBETTA_TS1
ReadConformPDB T0482.MQAX2-opt3.gromacs0.repack-nonPC.pdb	# < Pcons_dot_net_TS4 =? BAKER_ROBETTA_TS1
	# best rosetta energy

ReadConformPDB T0482.try2-opt3.pdb	# <MQAU1-opt3 < RBO-Proteus_TS1
# ReadConformPDB T0482.MQAU1-opt3.gromacs0.repack-nonPC.pdb	# < RBO-Proteus_TS1

ReadConformPDB T0482.MQAX4-opt3.pdb	# < GS-KudlatyPred_TS1

# ReadConformPDB T0482.try6-opt3.pdb	# < FALCON_TS5

ReadConformPDB T0482.try8-opt3.pdb  # < try3-opt3.gromacs0 < align(2exrA+1yckA+2fa1A+1v5dA+2opeA+2qx5A_1yckA)
# ReadConformPDB T0482.try3-opt3.gromacs0.pdb	# < align(2exrA+1yckA+2fa1A+1v5dA+2opeA+2qx5A_1yckA)

# ReadConformPDB T0482.MQAC1-opt3.pdb	# < SAM-T08-server_TS1

# ReadConformPDB T0482.try1-opt3.pdb	# < align(2ebdA)


InFilePrefix 
// ReadConformPDB T0482.undertaker-align.pdb model 1 # 2glwA
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0482.undertaker-align.pdb model 2 # 1zowA
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0482.undertaker-align.pdb model 3 # 2ebdA
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0482.undertaker-align.pdb model 4 # 1hnjA
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0482.undertaker-align.pdb model 5 # 1u6eA
# 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