[ccp4bb] Multiple sequence alignment (vs) multiple structure alignment

Hello, I am looking at insertions/deletions occurring at various places in my protein and also I want to map the active site residues. I have performed Multiple sequence alignment as well as multiple structure based alignment for my protein of study. I have obtained different alignment patterns

[ccp4bb] structure based superposition

Dear all, I would like to know the tools/servers/programs that can be used for structure based superposition of two or more proteins. Please help me out..!! Thanks, -Suda