Find gaps and warn; SEC mutant; renumber optional

1) Popup messageBox will warn users of gaps in the peptide sequence
(missing residues) that must be corrected for DMD to work
2) Deal with selenocysteine residues in the simplest way possible:
rename them as CYS and replace the Se with S. (This may not work if C -
S[e] - H distances are important. Will think on this more.)
3) Make renumbering the residues optional. User can elect to preserve
the numbering from the original PDB file, even if the residue numbering
does not begin with 1.