Let's say you want to know which residues in a protein are important for a particular function, so you can tweak them to improve function.
You could
- spend months or years solving a structure of the complex then look at the structure and look at the direct contacts - then mutate to various other resides to see if they affect function ( finding out that even with a structure of the complex your chosen list is far from 100% correct )
- look at sequence alignments and then make a library of millions of variants and screen in a couple of months.
The first feels better as the glorious scientist is doing 'rational design', however it can be much more hit and miss and slower and more expensive.
As I understand it, one of the things about Cryo-EM is it's potentially much faster/easier than previous methods - but even so, looking at the structure doesn't get you to the answer direct - it's still very much hit and miss.