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 T0493.a2m 1
 NameTarget T0493
// 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 T0493.try8-opt3.pdb # < chimera-try7-MQAU6 < chimera-MQAU4-try4 < try3-opt3.gromacs0 <try2-opt3 < try1-opt3 < align(1pjrA)
# ReadConformPDB T0493.try7-opt3.pdb # < chimera-MQAU4-try4 < try3-opt3.gromacs0 <try2-opt3 < try1-opt3 < align(1pjrA)
# ReadConformPDB T0493.try4-opt3.pdb # < try3-opt3.gromacs0 <try2-opt3 < try1-opt3 < align(1pjrA)
# ReadConformPDB T0493.try3-opt3.gromacs0.pdb # <try2-opt3 < try1-opt3 < align(1pjrA)
# ReadConformPDB T0493.try2-opt3.pdb # < try1-opt3 < align(1pjrA)

# ReadConformPDB T0493.MQAU6-opt3.pdb.gz	# < MUProt_TS4
ReadConformPDB T0493.MQAC4-opt3.gromacs0.repack-nonPC.pdb.gz	# < MUProt_TS4
# ReadConformPDB T0493.MQAC6-opt3.pdb.gz	# < MUProt_TS4

ReadConformPDB T0493.MQAU4-opt3.gromacs0.pdb.gz	# < MULTICOM-CLUSTER_TS1
# ReadConformPDB T0493.MQAC1-opt3.gromacs0.pdb.gz	# < MULTICOM-CLUSTER_TS1
# ReadConformPDB T0493.MQAU1-opt3.gromacs0.pdb.gz	# < MULTICOM-CLUSTER_TS1

ReadConformPDB T0493.try6-opt3.gromacs0.repack-nonPC.pdb # <try5-opt3.gromacs0.repack-nonPC < align(2is6A)
# ReadConformPDB T0493.try5-opt3.pdb # < align(2is6A)

ReadConformPDB T0493.try1-opt3.pdb # < align(1pjrA)


InFilePrefix 
// ReadConformPDB T0493.undertaker-align.pdb model 1	# 1pjrA
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0493.undertaker-align.pdb model 2	# 2is6A
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0493.undertaker-align.pdb model 3	# 1pjr
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0493.undertaker-align.pdb model 4	# 1w36B
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0493.undertaker-align.pdb model 5	# 1w36C
# 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