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 monomeric-50pc.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 T0222.a2m 
 NameTarget T0222
// Now have a random conformation---use PopConform if you don't want it.
 PopConform


Time

InFilePrefix 
ReadConformPDB 236-end/decoys/T0222.try3-opt2.pdb	# to get possible relationship between domains
ReadConformPDB 1-274/decoys/T0222.try6-opt2.pdb	# domain 1
ReadConformPDB 273-end/decoys/T0222.try3-opt2.pdb # domain 2

Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB domain-models.pdb superpose \
	atom Q273.N	atom Q273.CA	atom Q273.C \
	atom G274.N	atom G274.CA	atom G274.C 

# 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