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 TR429.a2m 22
 NameTarget TR429
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/



InFilePrefix  E22-A101/decoys/
ReadConformPDB TR429.try2-opt3.pdb name N-try2	# < TR429

InFilePrefix decoys/
ReadConformPDB TR429.try4-opt3.gromacs0.pdb	# < chimera-N3-try3

InFilePrefix  R100-P176/decoys/
ReadConformPDB TR429.try2-opt3.pdb name C-try2	# < TR429 

Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB for-chimera-N2-C2.pdb superpose