PDB Structure Aligner
Structural alignment of PDB protein sequences
Requires Geneious 4.8+
Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).
Once installed, run the plugin by selecting two protein structures and clicking on Align/Assemble - Protein Structure Alignment in the toolbar.