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 T0465.a2m 1
 NameTarget T0465
// 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 T0465.try11-opt3.pdb # < FALCON_CONSENSUS_TS2-scwrl.pdb

ReadConformPDB T0465.MQAC1-opt3.pdb	# < SAM-T08-server_TS1

ReadConformPDB T0465.MQAX4-opt3.gromacs0.repack-nonPC.pdb	# < BAKER-ROBETTA_TS3
xn	# best rosetta energy
# ReadConformPDB T0465.try19-opt3.pdb # < MQAX4-modified < MQAX4-opt3 < BAKER-ROBETTA_TS3
# ReadConformPDB T0465.try15-opt3.pdb 	# < MQAX4-opt3
# ReadConformPDB T0465.try14-opt3.pdb 	# < MQAX4-opt3

ReadConformPDB T0465.MQAX19-opt3.pdb	# < BAKER-ROBETTA_TS4


ReadConformPDB T0465.try20-opt3.pdb	# < align(2z69A?)

# ReadConformPDB T0465.try2-opt3.pdb	# < MQAX1-opt3 < BAKER-ROBETTA_TS5
# ReadConformPDB T0465.MQAX1-opt3.pdb	# < BAKER-ROBETTA_TS5

# ReadConformPDB T0465.try3-opt3.pdb	# < align(1svjA)



# ReadConformPDB T0465.MQAU1-opt3.pdb	# < SAM-T08-server_TS1
# ReadConformPDB T0465.try8-opt3.pdb # < FALCON_CONSENSUS_TS2-scwrl.pdb
# ReadConformPDB T0465.try7-opt3.pdb # < FALCON_CONSENSUS_TS2-scwrl.pdb
# ReadConformPDB T0465.try6-opt3.pdb # < FALCON_CONSENSUS_TS2-scwrl.pdb

# ReadConformPDB  FALCON_CONSENSUS_TS2-scwrl.pdb
#  PrintConformSheets falcon2.sheets
#  PrintConformHelices falcon2.helices



#  PrintConformSheets try3-opt3.sheets
#  PrintConformHelices try3-opt3.helices

#ReadConformPDB T0465.try4-opt3.pdb	# < align(1tggA)

#ReadConformPDB T0465.try1-opt3.repack-nonPC.pdb	# < align(1wdcB)

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

InFilePrefix 
#ReadConformPDB T0465.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
#ReadConformPDB T0465.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
#ReadConformPDB T0465.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0465.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0465.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