SetSeed

InfilePrefix 
// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/atoms-inputs/
ReadTrainingAtoms monomeric-50pc.atoms
ReadRotamerLibrary dunbrack-1332.rot

InFilePrefix /projects/kestrel/users/karplus/burial/undertaker/spots/
    ReadAtomType pdb-name.types
    ReadClashTable pdb-atom-name.clash
    SetClashDefinition pdb-atom-name

Time


//Need to read in target before specific fragments or alignments can
// be read, also before constraints can be defined.

InFilePrefix 

ReadTargetPDB decoys/whole-try11-chimera.pdb
NameTarget T0206

MakeGenericFragmentLibrary
Time

InFilePrefix 

Time

AddId 1jh5A 
AddId 1jh5B
AddId 1jh5C
ReadTemplatePDBIds 

InFilePrefix 81-end/1jh5A/
ReadFragmentAlignment NOFILTER 1jh5-trimer.a2m
InFilePrefix
PrintMultimerPDB 3 trimer-1jh5-whole-try11.pdb
Time