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 T0464.a2m 1
 NameTarget T0464
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/



InFilePrefix decoys/

ReadConformPDB T0464.try8-opt3.pdb	# < MQAU7-opt3 < SAM-T06-server_TS1
# ReadConformPDB T0464.MQAU7-opt3.pdb	# < SAM-T06-server_TS1
# ReadConformPDB T0464.MQAC7-opt3.pdb	# < SAM-T06-server_TS1	
# ReadConformPDB T0464.MQAU1-opt3.gromacs0.repack-nonPC.pdb	# < SAM-T06-server_TS1	
# ReadConformPDB T0464.MQAC1-opt3.gromacs0.pdb		# < SAM-T06-server_TS1	

ReadConformPDB T0464.MQAX7-opt3.pdb	# < Pcons_multi_TS1
# ReadConformPDB T0464.MQAX1-opt3.pdb	# < Pcons_multi_TS1
# ReadConformPDB T0464.MQAUC7-opt3.pdb	# < Pcons_multi_TS1


ReadConformPDB T0464.try7-opt3.pdb	# < try3-opt3 < align(2jwyA)
# ReadConformPDB T0464.try3-opt3.pdb	# < align(2jwyA)

# ReadConformPDB T0464.try5-opt3.gromacs0.pdb	# < align(2d0iA)
ReadConformPDB T0464.try1-opt3.gromacs0.pdb	# < align(1sgpI)

ReadConformPDB T0464.try2-opt3.gromacs0.repack-nonPC.pdb	# < align(2hf1A)

# ReadConformPDB T0464.try6-opt3.pdb		# < align(2jwyA)

# ReadConformPDB T0464.try4-opt3.gromacs0.pdb	# < align(2jnyA)

InFilePrefix 
# ReadConformPDB T0464.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
# ReadConformPDB T0464.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
# ReadConformPDB T0464.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0464.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0464.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