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 T0318.a2m 1
 NameTarget T0318
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/
// include read-pdb.under

# put believed-to-be-best decoy first


InFilePrefix decoys/
ReadConformPDB T0318.try3-opt2.pdb # optimized from chimera.pdb
ReadConformPDB chimera2.pdb	#try1 with N-terminus from servers
ReadConformPDB T0318.try1-opt2.pdb # fully automatic
ReadConformPDB chimera.pdb	#try1 with N-terminus separately predicted

InFilePrefix 
ReadConformPDB T0318.undertaker-align.pdb model 1	# from 1lam

# ReadConformPDB T0318.try4-opt2.gromacs0.repack-nonPC.pdb # the top monomer, based on server models for N-terminus

# ReadConformPDB T0318.try2-opt2.pdb # earlier version of try3


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 

# 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