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 T0321.a2m 1
 NameTarget // 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/
// include read-pdb.under

InFilePrefix decoys/
# choose one of try14 and try15
ReadConformPDB T0321.try14-opt2.pdb
ReadConformPDB T0321.try15-opt2.pdb

InFilePrefix decoys/
# choose one of try17 and try16
ReadConformPDB T0321.try17-opt2.pdb	#chimera, robetta5+try15-opt2
# ReadConformPDB T0321.try16-opt2.pdb	#chimera, robetta5+try15-opt2

# don't submit, just compare to try17 and try16
InFilePrefix decoys/servers/
# ReadConformPDB ROBETTA_TS5.pdb	# best-scoring of server models (except ours)


InFilePrefix decoys/
ReadConformPDB T0321.try12-opt2.pdb

InFilePrefix decoys/
ReadConformPDB T0321.try4-opt2.pdb

#	ReadConformPDB T0321.try11-opt2.pdb # too similar to try14-opt2
#	ReadConformPDB T0321.try9-opt2.pdb # too similar to try12-opt2


InfilePrefix M1-K123/decoys/
# ReadConformPDB T0321.try3-opt2.pdb
# ReadConformPDB T0321.try4-opt2.pdb


InfilePrefix V105-K251/decoys/
# ReadConformPDB T0321.try3-opt2.pdb


InFilePrefix 
# ReadConformPDB T0321.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
# ReadConformPDB T0321.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
# ReadConformPDB T0321.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
# ReadConformPDB T0321.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
# ReadConformPDB T0321.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 G129 residue P132 residue I146 residue E148 \
	residue T174 residue D180 residue T182 residue L186 \
	residue G200 \
	residue A80 residue N83 
	

# 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