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 T0443.a2m 1
 NameTarget T0443
// 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 T0443.try9-opt3.pdb.gz	# < try5-opt3 < try4-opt3 < BAKER-ROBETTA_TS1


# ReadConformPDB T0443.try7-opt3.pdb.gz	# < try5-opt3
# ReadConformPDB T0443.try5-opt3.pdb.gz # < try4-opt3 < BAKER-ROBETTA_TS1

ReadConformPDB T0443.try8-opt3.pdb.gz	# < chimera-zhang4-try7


ReadConformPDB T0443.MQAU1-opt3.repack-nonPC.pdb # < SAM-T08-server_TS1

ReadConformPDB T0443.try2-opt3.gromacs0.repack-nonPC.pdb # < MQAC1-opt3 < SAM-T08-server_TS1

ReadConformPDB T0443.try14-opt3.pdb # < chimera-try8-try13

# ReadConformPDB T0443.try1-opt3.pdb
# ReadConformPDB T0443.try1-init.pdb



InFilePrefix decoys/servers/
# ReadConformPDB BAKER-ROBETTA_TS1 
 #  PrintConformSheets robetta1.sheets
 
#ReadConformPDB BAKER-ROBETTA_TS3 

# ReadConformPDB Zhang-Server_TS3
#  PrintConformSheets zhang3.sheets
#  PrintConformHelices zhang3.helices

# ReadConformPDB Zhang-Server_TS4
#  PrintConformSheets zhang4.sheets
#  PrintConformHelices zhang4.helices

#ReadConformPDB Zhang-Server_TS5
#  PrintConformSheets zhang5.sheets
#  PrintConformHelices zhang5.helices

# ReadConformPDB PSI_TS3
#  PrintConformSheets psi3.sheets
#  PrintConformHelices psi3.helices

# ReadConformPDB MUFOLD-MD_TS1
#  PrintConformSheets mufold1.sheets
#  PrintConformHelices mufold1.helices

InFilePrefix 
// ReadConformPDB T0443.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0443.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0443.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0443.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0443.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