Maybe fixed the alignment bug???
For something like ~10% of all the PFAM families, the alignments between
PDB and teh reference sequence are coming in much less than 90%.

(These can be detected by running test.ExamineAlignments).

Since BLAST reported these are regions that should align at least 90%,
need to be go back and see why the global and local approaches are so
badly disagreeing.

(But not tonight).