Understanding Alpha Channels

So in some places you want transparency, partial or full. One example is the bottle for potions, acc003. In the BM, there is an alpha layer which controls transparency. You notice on the bottle that there's a texture, this is because there is a partial alpha on those parts. For example this is the texture with the alpha layer turned off. But you can see the light gray bits you would want to be partially transparent, so you can see liquid inside:

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The alpha you would want to apply to this would be a light gray. So in the following image you can see, that the darker the alpha, the more transparent:

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This is the alpha channel on its own:

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White = not transparent. Black = Fully transparent. Gray = kinda transparent. Experiment a bit and you'll find the right balance for your texture