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 T0467.a2m 1
 NameTarget T0467
// 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 T0467.MQAY4-opt3.pdb	# < Pcons_dot_net_TS5 =? BAKER-ROBETTA_TS5
ReadConformPDB T0467.try4-opt3.pdb	# < try2-opt3.gromacs0 < MQAY2-opt3 < BAKER-ROBETTA_TS1
	# this claims to be from BAKER-ROBETTA_TS1, but looks more
	#	like the TS5 models.  Perhaps there was crossover.
# ReadConformPDB T0467.MQAY1-opt3.pdb	# < BAKER-ROBETTA_TS5

# ReadConformPDB T0467.try2-opt3.pdb	# < MQAY2-opt3 < BAKER-ROBETTA_TS1
ReadConformPDB T0467.MQAY2-opt3.gromacs0.repack-nonPC.pdb	# < BAKER-ROBETTA_TS1
	# best rosetta energy

ReadConformPDB T0467.try9-opt3.pdb	# < try7-opt3 < chimera-MQAY2-try6
# ReadConformPDB T0467.try7-opt3.pdb	# < chimera-MQAY2-try6

ReadConformPDB T0467.try10-opt3.pdb	# < try8-opt3 < chimera-MQAY4-try6
# ReadConformPDB T0467.try8-opt3.pdb	# < chimera-MQAY4-try6

# ReadConformPDB T0467.try6-opt3.pdb 	# < T0468

# ReadConformPDB T0467.try3-opt3.pdb	# < align(1pfoA?)


# keep ONE of the 1vpmA models:

ReadConformPDB T0467.try5-opt3.pdb	# < MQAC1-opt3 < SAM-T08-server_TS1
# ReadConformPDB T0467.MQAC1-opt3.pdb	# < SAM-T08-server_TS1
# ReadConformPDB T0467.MQAU1-opt3.pdb	# < SAM-T08-server_TS1
# ReadConformPDB T0467.try1-opt3.pdb	# < align(1vpmA)




InFilePrefix decoys/servers/
// ReadConformPDB BAKER-ROBETTA_TS1
#    PrintConformSheets robetta1.sheets
#    PrintConformHelices robetta1.helices
 

InFilePrefix 
// ReadConformPDB T0467.undertaker-align.pdb model 1 # 1c8cA
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0467.undertaker-align.pdb model 2 # 1xyiA
# PrintConformSheets align2.sheets
# PrintConformHelices align2.
// ReadConformPDB T0467.undertaker-align.pdb model 3 # 2z1cA
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0467.undertaker-align.pdb model 4 # 1yliA
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0467.undertaker-align.pdb model 5 # 1azpA
# 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