ui.AlignGuide (or the interface Align Guide) does not align every segment but only some. The following code demonstrates:

function wait()
for x=1, 100000 do
end
end

for i = 1, structure.GetCount() do
ui.AlignGuide(i)
print("segment ",i)
wait()
end

(the wait is only to slow it down a bit)

I haven't been able to use align guide for anything as each alignment seems to occupy its own space and is not reachable from the protein space by bands. In other words, bands attached, for example, when the first segment is aligned are of no use when the last segment is aligned. Has anyone else found a use?