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Noob's quest: looking for the Alpha channel


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Greetings people, your newest noob here.

I have been trying to create textures for a custom 3D model for a certain game that I enjoy. I am about done and it doesn't look too bad actually, but now I have run into a problem. Apparently the game uses the alpha channel of the texture to determine where it will use the player colour instead of what is in the textures and I can't figure out how to tinker with it. Can I use Paint.net to do it at all? If yes, how? If not, what can I use instead?

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