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 

 ReadTargetPDB trimer-1jh5-whole-try11.pdb
 NameTarget T0206


Time

// include best previously found decoys!
InFilePrefix 

# put believed-to-be-best decoy first
ReadConformPDB 	T0206.3mer.ABC.d1.try1.d2.try6.dv3.pdb.gz
ReadConformPDB trimer-1jh5-whole-try11.pdb


Time


// Don't put superimposed models into decoys/
// since that could mess up programs that find all decoy files.
OutFilePrefix
printAllConformPDB trimers-superposed.pdb superpose \
	atom L81.CA atom N91.CA atom I101.CA atom G111.CA atom L121.CA \
	atom T131.CA

# 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