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 T0419.a2m 1
 NameTarget T0419
// 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 T0419.try11-opt3.repack-nonPC.pdb	# similar to try9-opt3
	# < chimera-try9-M2-C2-try10

ReadConformPDB T0419.try10-opt3.pdb	# replaces MQAC1-opt3
	# < MQAC1-opt3.gromacs0

ReadConformPDB T0419.try12-opt3.gromacs0.repack-nonPC.pdb	# same overall organization as try10-opt3
	# < chimera-try10-M2-C2
	
# ReadConformPDB	T0419.MQAC1-opt3.gromacs0.repack-nonPC.pdb
# PrintConformSheets MQAC1-opt3.sheets
# PrintConformHelices MQAC1-opt3.helices
	# < BAKER-ROBETTA_TS1


ReadConformPDB T0419.try9-opt3.pdb	# replaces try8-opt3
	# < try8-opt3.repack-nonPC
# ReadConformPDB T0419.try8-opt3.pdb	
	# < tweaked3-try7-opt3
	# try7 < try6-opt3.repack-nonPC < try5-opt3.exploded

# ReadConformPDB	T0419.try5-opt3.gromacs0.repack-nonPC.pdb
	# < chimera-N1-try4-M1-C1

ReadConformPDB	T0419.try4-opt3.gromacs0.repack-nonPC.pdb
	# < alignments (2plrA)

# the following have only one of the domains
// ReadConformPDB	T0419.MQAU1-opt3.repack-nonPC.pdb
// #  PrintConformSheets MQAU1-opt3.sheets
// #  PrintConformHelices MQAU1-opt3.helices
// ReadConformPDB T0419.try2-opt3.gromacs0.repack-nonPC.pdb
// ReadConformPDB T0419.try1-opt3.repack-nonPC.pdb


InFilePrefix 
// ReadConformPDB T0419.undertaker-align.pdb model 1
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0419.undertaker-align.pdb model 2
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
// ReadConformPDB T0419.undertaker-align.pdb model 3
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
// ReadConformPDB T0419.undertaker-align.pdb model 4
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0419.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 V42 residue I43 \
# 	residue I44 residue L45 \
# 	residue I46 residue N47 residue G48

# 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