SetSeed

// Note: the training atoms are needed for patching up chain breaks
// when reading in conformations.
InFilePrefix /projects/compbio/experiments/undertaker/atoms-inputs/
ReadTrainingAtoms dunbrack-2191.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 XXX0000.a2m START_COL
# ReadTargetPDB XXX0000.blank.pdb
NameTarget XXX0000
// 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 
Include XXX0000.t2k.undertaker-align.under

// May want to add extra arguments to the following, to 
//	specify highly conserved residues or atoms to focus on when superposing.
PrintAlignmentsPDB XXX0000.t2k.undertaker-align.pdb superpose
PrintAlignmentsSheets XXX0000.t2k.undertaker-align.sheets

quit