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During the final fight sequence between Spock and Khan. Spock applies the Vulcan nerve pinch to Khan, who lets out a scream of pain but doesn't collapse.

Why didn't the nerve pinch work?

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Changed the title, since I for myself was very glad that I didn't know Khan was part of the movie until I watched it and maybe others would be, too. –  Napoleon Wilson Jun 2 '13 at 11:36
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In the original series "Assignment: Earth", the human derived from a hidden planet, Gary Seven, shrugs off a Vulcan nerve pinch without any discomfort at all.

Khan is not incapacitated by it, but does create much pain for him—so presumably it would be worse for anyone else. We don't know if his superior muscularity guards the nerves or if his genetically engineered nervous system is better able to cope with the paralysis effects normal to humans.

Presumably then, the maneuver is most effective on more weakly engineered humans. The most advanced are less affected by it.

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I personally think it has to do with his superior nervous system. Earlier in the movie we see him take a phaser straight on and it didn't slow him down all that much. Only consecutive shots really had an affect. –  DForck42 Jun 3 '13 at 13:53
    
@DForck42 - see my comment below - It's worked on other Eugenics humans of the same "breed" as Khan in 'Space Seed'. –  JohnP Jun 3 at 14:38
    
Later in the movie, when on board the Dreadnought class ship, he takes a stun shot from a phaser on the bridge and goes down immediately, while the effects weren't lasting it knocked him out completely. –  BB Stacker Jun 4 at 12:43
    
@BBStacker - One wonders, then, why he wasn't felled by the multiple stun shots fired by Uhura on the floating barge later in the movie? –  JohnP Jun 4 at 14:27
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Spock's Vulcan Nerve Pinch was much less effective on Khan, due to his superior genetic engineering. Although, it had a temporary painful effect, Khan, as stated in the film, was the most dangerous adversary they have/had ever faced.

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What does being a dangerous adversary have to do with it? Also, in 'Space Seed' (ST:TOS), the original appearance of Khan, one of the engineered humans is subdued instantly by Spock using the nerve pinch. –  JohnP Jun 3 at 14:37
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Interesting...There is an inconsistency with the new and old then. –  BB Stacker Jun 4 at 12:35
    
Heh...that's hardly news. :) –  JohnP Jun 4 at 14:25
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