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 T0496.a2m 1
 NameTarget T0496
// 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 T0496.try7-opt3.pdb # < chimera-try6-try3

ReadConformPDB T0496.try6-opt3.pdb	# < try2-opt3 < try1-opt3 < align(1ryp2+2f9iB+2chcA+1ixsA+2i9cA)
# ReadConformPDB T0496.try2-opt3.pdb		# < try1-opt3
# ReadConformPDB T0496.try1-opt3.gromacs0.pdb	# < align(1ryp2+2f9iB+2chcA+1ixsA+2i9cA)



ReadConformPDB T0496.try12-opt3.gromacs0.repack-nonPC.pdb	# < MQAY8-opt3.repack-nonPC < Pcons_dot_net_TS3=BAKER-ROBETTA_TS4
	# best rosetta score
# ReadConformPDB T0496.try11-opt3.pdb	# < MQAY8-opt3.repack-nonPC < Pcons_dot_net_TS3=BAKER-ROBETTA_TS4
# ReadConformPDB T0496.MQAY8-opt3.pdb	# < Pcons_dot_net_TS3=BAKER-ROBETTA_TS4
# ReadConformPDB T0496.MQAY9-opt3.pdb	# < Pcons_dot_net_TS3=BAKER-ROBETTA_TS4



# ReadConformPDB T0496.try3-opt3.gromacs0.pdb	# < align(1neuA+2f9iB+1ibrB+2i1mA+3bqoA+1ixsA+1q2hA)

ReadConformPDB T0496.try4-opt3.gromacs0.pdb	# < align(1egaA+1p0zA+1ixsA+2f9iB+1q2hA+2i9cA+1ht6A)


ReadConformPDB T0496.try5-opt3.gromacs0.repack-nonPC.pdb	# <MQAY1-opt3 < Pcons_dot_net_TS5=BAKER-ROBETTA_TS5
	# second best Rosetta energy
# ReadConformPDB T0496.MQAY1-opt3.gromacs0.repack-nonPC.pdb	# < Pcons_dot_net_TS5
#  PrintConformSheets MQAY1.sheets
#  PrintConformHelices MQAY1.helices


# ReadConformPDB T0496.MQAX8-opt3.pdb	# < SAM-T08-server_TS1
# ReadConformPDB T0496.MQAC1-opt3.gromacs0.pdb	# < SAM-T08-server_TS1
# ReadConformPDB T0496.MQAU1-opt3.pdb	# < SAM-T08-server_TS1


# ReadConformPDB T0496.MQAX10-opt3.pdb	# < RAPTOR_TS3-scwrl
#	Too broken to be worth polishing.


# InFilePrefix decoys/servers/
# ReadConformPDB RAPTOR_TS1
#  PrintConformSheets raptor1.sheets
#  PrintConformHelices raptor1.helices
# ReadConformPDB RAPTOR_TS2
#  PrintConformSheets raptor2.sheets
#  PrintConformHelices raptor2.helices
# ReadConformPDB RAPTOR_TS3
#  PrintConformSheets raptor3.sheets
#  PrintConformHelices raptor3.helices
# ReadConformPDB RAPTOR_TS4
#  PrintConformSheets raptor4.sheets
#  PrintConformHelices raptor4.helices
# ReadConformPDB RAPTOR_TS5
#  PrintConformSheets raptor5.sheets
#  PrintConformHelices raptor5.helices
# 
# ReadConformPDB Zhang-Server_TS2
#  PrintConformSheets zhang2.sheets
#  PrintConformHelices zhang2.helices



InFilePrefix 
// ReadConformPDB T0496.undertaker-align.pdb model 1 # < 2f9iB
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0496.undertaker-align.pdb model 2 # < 2csoA
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0496.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0496.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0496.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 G57 residue L58 residue V59 residue M60 residue S61 \
	residue A62 residue N63 residue C64 residue V65 residue K66 \
	residue D67 residue T68 residue P69 residue F70 residue H71 \
	residue F72 residue F73 residue K74

# 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