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 TR432.a2m 1
 NameTarget TR432
// 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
ReadConformPDB TR432.try7-opt3.pdb	# < chimera-try6-try5
	# best undertaker score
	
ReadConformPDB TR432.try7-opt3.gromacs0.repack-nonPC.pdb	# < chimera-try6-try5
	# best with rosetta energy

ReadConformPDB TR432.try6-opt3.pdb	# < chimera-try4-MULTICOM

ReadConformPDB TR432.try5-opt3.pdb	# < try3-opt3 < try2-opt3.gromacs0.repack-nonPC < chimera-init-try1

ReadConformPDB TR432.try4-opt3.repack-nonPC.pdb	# < TR432
	# optimized directly from provided model

# ReadConformPDB TR432.try2-opt3.gromacs0.pdb # < chimera-init-try1
	# Earlier version for making try5

# ReadConformPDB TR432.pdb
#  PrintConformSheets init.sheets
#  PrintConformHelices init.helices

# ReadConformPDB TR432.try1-opt3.pdb # < align(1pytA?)

InFilePrefix ../T0432/decoys/servers/
# ReadConformPDB LEE-SERVER_TS1
# ReadConformPDB Phyre_de_novo_TS1
# ReadConformPDB FEIG_TS1
# ReadConformPDB MULTICOM-REFINE_TS2
# ReadConformPDB Zhang-Server_TS2
# ReadConformPDB COMA-M_TS4
# ReadConformPDB keasar-server_TS3

InFilePrefix 
// ReadConformPDB TR432.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB TR432.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB TR432.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB TR432.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB TR432.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