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-1332.rot


InFilePrefix /projects/compbio/experiments/undertaker/spots/
#    ReadAtomType pdb-name.types
#    ReadClashTable pdb-1332-2symm.clash
#    SetClashDefinition pdb-2symm
    ReadAtomType exp-pdb.types
    ReadClashTable exp-pdb-1332-2symm.clash
    SetClashDefinition exp-pdb-2symm

Time


//Need to read in target before specific fragments or alignments can
// be read, also before constraints can be defined.

InFilePrefix 

 ReadTargetSeq T0262.a2m 
 NameTarget T0262
// 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

InFilePrefix 75-200/decoys/
ReadConformPDB T0262.try3-opt2.pdb

InFilePrefix 1-85/decoys/
ReadConformPDB T0262.try2-opt2.pdb

InFilePrefix 190-256/decoys/
ReadConformPDB T0262.try2-opt2.pdb

InFilePrefix
Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB T0262.superpose.d2-try3.d1-try2.d3-try2.pdb superpose \
	residue T78 residue L79 residue A80 residue G81 residue T192 residue S193 residue S194 residue L195

# Can specify a set of residues as optional arguments of printAllConformPDB
# to give initial set of residues to align.
# Format: 	residue A7	residue K252	...

Time

quit