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 TR461.a2m 20
 NameTarget TR461
// 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/

# family of models from TR461

ReadConformPDB TR461.try27-opt3.pdb	# < try15-opt3 < try10-opt3.gromacs0 < try5-opt3 < try4-opt3.gromacs0 < try2-opt3 < TR461
# ReadConformPDB TR461.try33-opt3.pdb	# < try15-opt3 < try10-opt3.gromacs0 < try5-opt3 < try4-opt3.gromacs0 < try2-opt3 < TR461
# ReadConformPDB TR461.try15-opt3.pdb	# < try10-opt3.gromacs0 < try5-opt3 < try4-opt3.gromacs0 < try2-opt3 < TR461
# ReadConformPDB TR461.try10-opt3.pdb	# < try5-opt3 < try4-opt3.gromacs0 < try2-opt3 < TR461
# ReadConformPDB TR461.try5-opt3.pdb	# < try4-opt3.gromacs0 < try2-opt3 < TR461
# ReadConformPDB TR461.try4-opt3.pdb	# < try2-opt3 < TR461
# ReadConformPDB TR461.try2-opt3.gromacs0.pdb	# < TR461

ReadConformPDB TR461.try34-opt3.pdb	# < try29-opt3.gromacs0 <try21-opt3 < chimera-try15-try18	(late loop from try18)
# ReadConformPDB TR461.try29-opt3.pdb	# <try21-opt3 < chimera-try15-try18	(late loop from try18)
# ReadConformPDB TR461.try21-opt3.pdb	# < chimera-try15-try18	(late loop from try18)



ReadConformPDB TR461.try28-opt3.pdb	# < try22-opt3 < chimera-try15-try19	(late loop from try19)
# ReadConformPDB TR461.try22-opt3.pdb	# < chimera-try15-try19	(late loop from try19)

ReadConformPDB TR461.try32-opt3.pdb	# < try23-opt3 < chimera-try15-try17	(late loop from try17)
# ReadConformPDB TR461.try23-opt3.pdb	# < chimera-try15-try17	(late loop from try17)

ReadConformPDB TR461.try30-opt3.pdb	# < try20-opt3  < chimera-try15-try16 (early loop from try16)
# ReadConformPDB TR461.try20-opt3.pdb	# < chimera-try15-try16 (early loop from try16)

# ReadConformPDB TR461.try31-opt3.pdb	# < try24-opt3 < chimera-try20-try21 
# ReadConformPDB TR461.try24-opt3.pdb	# < chimera-try20-try21 

# ReadConformPDB TR461.try26-opt3.pdb	# < chimera-try20-try17
# ReadConformPDB TR461.try25-opt3.pdb	# < chimera-try20-try19



# family of models from 2nx8A (for alternate loop models)

# ReadConformPDB TR461.try19-opt3.pdb	# < try14-opt3.gromacs0 < try1-opt3.gromacs0 < align(2nx8A)
# ReadConformPDB TR461.try14-opt3.gromacs0.pdb	# < try1-opt3.gromacs0 < align(2nx8A)
# ReadConformPDB TR461.try1-opt3.gromacs0.pdb	# < align(2nx8A)


# ReadConformPDB TR461.try17-opt3.pdb	# < try12-opt3.gromacs0 < try3-opt3. gromacs0 < align(2nx8A)
# ReadConformPDB TR461.try12-opt3.pdb	# < try3-opt3. gromacs0 < align(2nx8A)
# ReadConformPDB TR461.try12-opt3.gromacs0.repack-nonPC.pdb	# < try3-opt3. gromacs0 < align(2nx8A)
	# second best Rosetta energy  (but not great zinc site)
# ReadConformPDB TR461.try3-opt3.gromacs0.repack-nonPC.pdb	# < align(2nx8A)
	# best Rosetta energy (but not great zinc site)

# ReadConformPDB TR461.try16-opt3.pdb	# < try11-opt3.gromacs0 < try9-opt3 < try6-opt3 < align(2nx8A)
# ReadConformPDB TR461.try11-opt3.pdb	# < try9-opt3 < try6-opt3 < align(2nx8A)
# ReadConformPDB TR461.try9-opt3.pdb	# < try6-opt3 < align(2nx8A)
# ReadConformPDB TR461.try6-opt3.pdb	# < align(2nx8A)

# ReadConformPDB TR461.try18-opt3.pdb	# < try13-opt3.gromacs0 < try7-opt3 < align(2nx8A)
# ReadConformPDB TR461.try13-opt3.pdb	# < try7-opt3 < align(2nx8A)
# ReadConformPDB TR461.try7-opt3.pdb	# < align(2nx8A)

# ReadConformPDB TR461.try8-opt3.pdb	# < align(2nx8A) (rather junky)



# ReadConformPDB TR461.pdb
# PrintConformSheets init.sheets
# PrintConformHelices init.helices




InFilePrefix 
// ReadConformPDB TR461.undertaker-align.pdb model 1	# 2nx8A
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB TR461.undertaker-align.pdb model 2	# 2b3jA
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB TR461.undertaker-align.pdb model 3	# 1z3aA
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB TR461.undertaker-align.pdb model 4	# 1wwrA
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB TR461.undertaker-align.pdb model 5	# 1wkqA
# 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