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 T0480.a2m 1
 NameTarget T0480
// 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/


# trying to get zinc-binding site:

ReadConformPDB	T0480.try10-opt3.pdb	# < MQAU5-opt3 < RBO-Proteus_TS4
# ReadConformPDB T0480.MQAU5-opt3.pdb	# < RBO-Proteus_TS4

ReadConformPDB T0480.try11-opt3.pdb # < try9-opt3 < try8-opt3.gromacs0 < align(2bmoA)
# ReadConformPDB T0480.try9-opt3.pdb # < try8-opt3.gromacs0 < align(2bmoA)
# ReadConformPDB T0480.try8-opt3.gromacs0.pdb # < align(2bmoA)

ReadConformPDB T0480.try5-opt3.pdb # < align(2hf1A)

ReadConformPDB T0480.try4-opt3.pdb # < align(1v6kA)

ReadConformPDB	T0480.MQAC5-opt3.gromacs0.pdb	# < SAM-T08-server_TS1

# ReadConformPDB T0480.try6-opt3.gromacs0.pdb # < align(2ct7A)

# ReadConformPDB T0480.try7-opt3.gromacs0.pdb # < align(2ct7A)


# maybe_metal, maybe_ssbonds

# ReadConformPDB	T0480.MQAU1-opt3.gromacs0.pdb	# < SAM-T08-server_TS1
# ReadConformPDB	T0480.MQAC1-opt3.gromacs0.pdb	# < SAM-T08-server_TS1

// # trying for disulfides:
// 
// ReadConformPDB T0480.try2-opt3.pdb # < try1-opt3 <  align(1v6kA)
// # ReadConformPDB T0480.try1-opt3.pdb # <  align(1v6kA)
// 
// ReadConformPDB T0480.try3-opt3.pdb	# < align(2bmoA)


InFilePrefix 
// ReadConformPDB T0480.undertaker-align.pdb model 1	# < 2ausB
# PrintConformSheets align1.sheets
# PrintConformHelices align1.helices
// ReadConformPDB T0480.undertaker-align.pdb model 2	# < 2apoB
# PrintConformSheets align2.sheets
# PrintConformHelices align2.helices
#  ReadConformPDB T0480.undertaker-align.pdb model 3	# < 1rlyA
# PrintConformSheets align3.sheets
# PrintConformHelices align3.helices
# ReadConformPDB T0480.undertaker-align.pdb model 4	# < 2ct7A
# PrintConformSheets align4.sheets
# PrintConformHelices align4.helices
// ReadConformPDB T0480.undertaker-align.pdb model 5 	# < 2e72A
# PrintConformSheets align5.sheets
# PrintConformHelices align5.helices

# ReadConformPDB T0480.undertaker-align.pdb model 7 	# < 2bmoA



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 C21 residue C24 residue C39 residue C42

# 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