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-1332.atoms
ReadRotamerLibrary dunbrack-1332.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 T0358.a2m
ReadTargetPDB T0358.blank.pdb
NameTarget T0358
// 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 T0358.t2k-2track-undertaker.a2m

InFilePrefix 
Include T0358.t06.undertaker-align.under
Include T0358.t04.undertaker-align.under
Include T0358.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 T0358.t06.undertaker-align.pdb superpose

PrintAlignmentsPDB T0358.t04.undertaker-align.pdb superpose

PrintAlignmentsPDB T0358.t2k.undertaker-align.pdb superpose

quit