Does Chimera allow to display multiple protein structures as CA trace, colour corresponding residues in 3d, display these proteins' sequences in alignment window and allow to manually alter the alignment to manually align residues coloured as mutually corresponding (preferably by mouse)? Something like was possible in good old and unfortunately not supported any more Insight program... That's what wraps up to so-called structure-based manual multiple sequence alignment. Essential if you're assessing some highly diversified set of structures and want to have a precise alignment for them.

Thanks,

Kamil