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 TR464.a2m 18
 NameTarget TR464
// 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 from-dimer-try23-repack.pdb.gz # < dimer-try20-try22
# ReadConformPDB TR464.try20-opt3.pdb	# < try18-opt3 < chimera-try16-try17
# ReadConformPDB TR464.try18-opt3.pdb	# < chimera-try16-try17
# ReadConformPDB TR464.try19-opt3.pdb	# < try18-opt3.gromacs0.repack-nonPC < chimera-try16-try17


ReadConformPDB TR464.try16-opt3.pdb	# < try15-opt3 < try14-opt3.gromacs0.repack-nonPC < try13-opt3.gromacs0 <  chimera-try5-try12
# ReadConformPDB TR464.try15-opt3.pdb	# < try14-opt3.gromacs0.repack-nonPC < try13-opt3.gromacs0 <  chimera-try5-try12
# ReadConformPDB TR464.try14-opt3.pdb	# < try13-opt3.gromacs0 <  chimera-try5-try12
# ReadConformPDB TR464.try13-opt3.pdb	# <  chimera-try5-try12
# ReadConformPDB TR464.try12-opt3.pdb	# <  chimera-try5-try9

ReadConformPDB TR464.try11-opt3.pdb	# < try10-opt3 < chimera-try5-try9
# ReadConformPDB TR464.try10-opt3.pdb	# < chimera-try5-try9

ReadConformPDB TR464.try5-opt3.pdb	# < try4-opt3.gromacs0 < chimera-try2-MQAU1
# ReadConformPDB TR464.try4-opt3.gromacs0.repack-nonPC.pdb	# < chimera-try2-MQAU1
# ReadConformPDB TR464.try3-opt3.pdb	# < chimera-try2-MQAU1

ReadConformPDB TR464.try2-opt3.gromacs0.repack-nonPC.pdb	# < TR464
	# best rosetta score
# ReadConformPDB TR464.try2-opt3.pdb	# < TR464
# ReadConformPDB TR464.pdb
# PrintConformSheets init.sheets
# PrintConformHelices init.helices

# ReadConformPDB TR464.try17-opt3.pdb	# < aligh(2pk7A)

# ReadConformPDB TR464.try9-opt3.pdb	# < try8-opt3 < chimera-try2-try7
# ReadConformPDB TR464.try8-opt3.pdb	# < chimera-try2-try7


# ReadConformPDB TR464.try6-opt3.pdb	# < align(2hf1A)
# ReadConformPDB TR464.try7-opt3.pdb	# < align(2hf1A)

// ReadConformPDB TR464.try1-opt3.pdb	# < align(2j6aA+1k7jA+2hf1A+2ek5A+2gfgA)
# ReadConformPDB TR464.try1-init.pdb

// ReadConformPDB from-MQAUC7-opt3-gromacs.pdb.gz
// ReadConformPDB from-MQAX1-opt3.pdb.gz
// ReadConformPDB from-MQAU1-opt3.pdb.gz
// ReadConformPDB from-SAM-T06-server1.pdb.gz


InFilePrefix 
// ReadConformPDB TR464.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB TR464.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB TR464.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB TR464.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB TR464.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 G36 residue T37 residue V38 \
	residue N47 residue Q48 residue S49

# 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