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 T0305.a2m 1
 NameTarget T0305
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/
// include read-pdb.under

InFilePrefix decoys/
# put believed-to-be-best decoy first
ReadConformPDB T0305.try1-opt2.pdb
ReadConformPDB T0305.try2-opt2.pdb
ReadConformPDB from-tetramer-try1-opt2.pdb
ReadConformPDB dimer-try4-1rpmA.pdb
ReadConformPDB from-tetramer-try4-1larA.pdb
# ReadConformPDB dimer-try4-2fh7A.pdb




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 F27 \
	residue V30 \
	residue L68 \
	residue Y81 \
	residue V87 \
	residue I97 \
	residue P102 \
	residue F110 \
	residue W111 \
	residue I114 \
	residue I122 \
	residue Y139 \
	residue W140 \
	residue P141 \
	residue V153 \
	residue W201 \
	residue P207 \
	residue V233 


# 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