[Wintermute]

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Also, what about the fact that I'm getting almost 5:1 from the main pot? (So that if I can beat the other big stack, I virtually have to call?)

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Winter,
I am not sure that I really understand what you are getting at with this statement. You have to beat both the big stack and the all-in player for high to win 1/2 of the main pot (one or both undoubtedly have some kind of low). If the main pot is laying you 5:1, you true pot odds for 1/2 the main pot are 2:1 (you pay one to win half of six, for a profit of two). In the sidepot, you are at best getting your money back (if you beat the big stack for high, he must have a low or he is clinically insane). In sum, you need to beat both players for high to make a small profit in the sidepot, and you at best get your money back in the main pot.

I wouldn't rule out an A high flush, because the majority of players would slowplay an A2s on the turn in this hand. It is also quite possible that someone filled up on the river with a hand like A345 or 2345. I think calling here is a big-time losing proposition in the long run.

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I'm starting to lean your way but still not totally convinced--I realize that I'm only playing for half the main pot, and only then if I can beat the other big stack for high... but I just can't see him here w/ the nut flush, even w/ A2s for low. The flop action wouldn't make sense then. I figured the only way I was screwed is if the big stack caught a full house, and if he didn't then the 2:1 on the high half of the main pot is enough for me to call the short stack down. Meh, sounds a little wishy-washy to me now... this does look bad long-run.

FWIW:

Hero calls [$377].
Villian shows [ 8c, 2s, Ah, 7h ] two pairs, eights and threes.
Villian shows 8,5,3,2,A for low.
Shortstack shows [ 4s, 6s, 4c, Ad ] a flush, jack high.
Shortstack shows 8,5,4,3,A for low.
Hero shows [ Qs, 9h, Ks, Jh ] a flush, king high.
Hero wins $239.47 from side pot #1 with a flush, king high with king kicker.
Villian wins Lo ($239.47) from side pot #1 with 8,5,3,2,A.
Hero wins $394.80 from the main pot with a flush, king high with king kicker.
Villian wins Lo ($394.79) from the main pot with 8,5,3,2,A.