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 T0208.a2m
ReadTargetPDB T0208.blank.pdb
NameTarget T0208
// 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 T0208.t2k-2track-undertaker.a2m

InFilePrefix 

ReadFragmentAlignment 1a0dA/T0208-1a0dA-try3.vast-a2m	NOFILTER SCWRL
ReadFragmentAlignment 1gw9A/T0208-1gw9A-try3.vast-a2m	NOFILTER SCWRL
ReadFragmentAlignment 1nar/T0208-1nar-try9.vast-a2m	NOFILTER SCWRL
ReadFragmentAlignment 1k87A/T0208-1k87A-try9.vast-a2m	NOFILTER SCWRL
ReadFragmentAlignment 1reqA/T0208-1reqA-super.vast-a2m	NOFILTER SCWRL
ReadFragmentAlignment 1de5A/T0208-1de5A-super.vast-a2m	NOFILTER SCWRL
ReadFragmentAlignment 1a0dA/T0208-1a0dA-super.vast-a2m	NOFILTER SCWRL

// Include T0208.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 T0208.align-vast.pdb superpose

quit