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 T0248.a2m 
 NameTarget T0248
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/

InFilePrefix 
ReadConformPDB first-helix.pdb

InFilePrefix decoys/
ReadConformPDB T0248.try13-opt2.pdb



Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB first-helix+try13.pdb superpose \
	residue F19 residue A20 residue s21 residue Y22 residue K23 \
	residue E24 residue L25 residue R26 residue E27 residue A28 \
	residue F29 residue N30 residue D31
	

# 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