This requires a few things, Photoshop, and an edit of an .rs file, which is the shader file for the standardmesh of an object.
First in photoshop you want to go to the channels tab, once there you want to make a new channel, it will be called Alpha 1, Alpha 1 will appear black, this means currently the entire texture will be transparent. In order to get things not to be transparent, you need to copy their shape onto the black alpha channel, and adjust their shade. The closer to white you get, the more opaque that part of the texture will become, the more black, the more transparent.
Then once you've saved your .dds file as a RGBA, I use Interpolated Alpha for my save, you are going to need to edit the .rs file where that texture is applied. So lets say you have a standardmesh named Glass.sm, there should be a Glass.rs, open that .rs with Notepad, and look for the part where the texture is defined. In that textures code you simply need to add the line
transparent true;
to the shader, and save it. Now pack it all up and try it out!
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