sequences containing lowercase letters are not properly associated with their pdb files

Reported by Ian Holmes on Jalview discuss: http://www.jalview.org/pipermail/jalview-discuss/2011-August/000661.html

If a sequence is in lower case, then when its associated structure is opened, the structure will not be coloured in the same way as the sequence, and the corresponding positions will not be highlighted when the mouse is moved over them.

Also, opening the 'View mapping' report for the alignment between a lower case sequence and pdb structure reports a correct (case-independent) alignment but a lower %age identity (because upperCase/lowerCase is considered a mismatch).