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 T0467.a2m 1
 NameTarget T0467
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

OutfilePrefix decoys/


InFilePrefix decoys/
ReadConformPDB T0467.MQAY1-opt3.pdb	# < BAKER-ROBETTA_TS5
ReadConformPDB T0467.MQAC1-opt3.pdb	# < SAM-T08-server_TS1


Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB for-MQAY1-MQAC1.pdb superpose \
	residue Y35 residue E36 residue Y37 residue K38 \
	residue L39 residue T40 
	
# 	residue G41 residue F42 residue D43
# 	residue K44 residue D45 residue G46 residue K47 \
# 	residue E48 residue K49 residue E50

# 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