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-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 

ReadTargetSeq YBR225W.a2m
NameTarget YBR225W
// Now have a random conformation---use PopConform if you don't want it.

PopConform // get rid of random conformation

Time

MakeGenericFragmentLibrary
Time


// The following alignments are believed to be good:
// InFilePrefix 
// ReadFragmentAlignment YBR225W.t2k-2track-undertaker.a2m

InFilePrefix 
Include YBR225W.t2k.undertaker-align.under

PrintAlignmentsPDB YBR225W.t2k.undertaker-align.pdb superpose

quit