The selection cannot be removed with the Clear Atom Selection in track A, but also persists in track B and cannot be removed there either… It remains active, even when rotating the camera so it is not a blob on the screen, it is a selection on the ligand itself.
Track a:
And when switching to track b:
You can click on the icon in the lower right of the Small Molecule Design window (it has two blue balls connected by a line, as well as some other balls and lines) to remove it. You are right that it shouldn't persist between tracks, however.
Thank you for trying to resolve the issue, but I already tried that. That is why I wrote in my original post : "The selection cannot be removed with the Clear Atom Selection".
Oh, is that what that thing is called? My bad.