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 T0312.a2m 1
# ReadTargetPDB T0312.blank.pdb
NameTarget T0312
// 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 1xv2A/T0312-1xv2A-hand1.a2m NOFILTER SCWRL e_value 0.007
ReadFragmentAlignment 1xv2A/T0312-1xv2A-VAST-try6.a2m NOFILTER SCWRL e_value 1.


// May want to add extra arguments to the following, to 
//	specify highly conserved residues or atoms to focus on when superposing.
PrintAlignmentsPDB T0312.hand-align.pdb superpose
PrintAlignmentsSheets T0312.hand-align.sheets

quit