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 T0303.a2m 1
 NameTarget T0303
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

// include best previously found decoys!
InFilePrefix decoys/
OutfilePrefix decoys/
// include read-pdb.under

# put believed-to-be-best decoy first
ReadConformPDB T0303.try9-opt2.pdb	# opt from chimera1 with constraints
ReadConformPDB T0303.try10-opt2.pdb	# opt from chimera2 with constraints
ReadConformPDB T0303.try3-opt2.pdb	# opt from servers
ReadConformPDB T0303.try4-opt2.pdb	# opt with constraints on helices
# ReadConformPDB T0303.try1-opt2.pdb

InFilePrefix N17-R95/decoys/
# ReadConformPDB T0303.try3-opt2.pdb	# subdomain

InFilePrefix 
ReadConformPDB T0303.undertaker-align.pdb model 1
# ReadConformPDB T0303.undertaker-align.pdb model 2
# ReadConformPDB T0303.undertaker-align.pdb model 3
# ReadConformPDB T0303.undertaker-align.pdb model 4
# ReadConformPDB T0303.undertaker-align.pdb model 5

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 S18 residue L19 residue I93 residue N92

# 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