I have three complexes, and I need to do their superimpose through the substrate, which is identical for all three complexes. I unchecked the older not wanted tethers, but keeped (not delete) them for future usage. Thus I setup new six tethers and superimposed by tethers, that works; however, when I inspect the result, it is obviously wrong - the substrates are not superimposed as tight as they obviously can be.

I found that the superimpose takes in to calculation also the tethers, which are unchecked - is it bug? If they are removed completely then the result is much bether but still not perfect.

How to superimposed them more tightly?