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 T0281.a2m
ReadTargetPDB T0281.blank.pdb
NameTarget T0281
// Now have a random conformation---use PopConform if you don't want it.

PopConform // get rid of random conformation

Time

MakeGenericFragmentLibrary
Time


InFilePrefix 
ReadFragmentAlignment 1bf5A/1bf5A-T0281-try6-vast.a2m
ReadFragmentAlignment 1bylA/1bylA-T0281-try6-vast.a2m
ReadFragmentAlignment 1ecsA/1ecsA-T0281-try6-vast.a2m
ReadFragmentAlignment 1hh1A/1hh1A-T0281-try6-vast.a2m
ReadFragmentAlignment 1r9cA/1r9cA-T0281-try6-vast.a2m
ReadFragmentAlignment 1xan/1xan-T0281-try6-vast.a2m

// May want to add extra arguments to the following, to 
//	specify highly conserved residues or atoms to focus on when superposing.
PrintAlignmentsPDB T0281.vast-align.pdb superpose

quit