Ok, I'm tryin to use the perfect polygon and pipe tutorials to kame that cool doughnut pipe,

I can do all the cleaving, n stuff, but when I come to align the rotated sectors they wont match up, not even close, not even with the snap set too its smallest,

so, I was wonderin, is it possible to change the index vertice of a sector to allow for better alighning, if not, what am I doin wrong

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Ok, first of all, you are trying to line one tube up to the other, no? If that's so, then try moving the other sector a little first, so that is snaps to the grid (because it may not be snapped to the grid, which would thereby make it nearly impossible to align)

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Go to vertex mode and select the vertex you want the grid aligned to. Thin hit shift+s.

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