highlight positions in structures associated with many aligned transcripts

Mousing over ruler in a locus/multilocus alignment view could also (like with JAL-3982) highlight associated positions 3D structure views. At the very least, mousing over a linked CDS alignment's ruler should behave similarly to mousing over the protein alignment's ruler.

Estrogen CDS/protein alignment examples/estrogenReceptorProtein_aln.fa is a good example for this. Import and link the CDS/protein alignments, then show structures superposed - mouseover on ruler of CDS should highlight positions in protein structure...