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Re: [pygame] Per Pixel Alpha
you weren't changing the alpha value btw. the sequence for set_at is R,G,B,A you had 255,0,0,0 try 255,0,0,128
http://www.pygame.org/docs/ref/surface.html#Surface.set_at
This link is right on the pygame site. This reference list is brilliant and explains how to use pygame very well.
If you want to modify a lot of inividual pixel values really fast then use Surfarray. I can't remember if there was another method as well.