I have a large object with many parts that Im baking out in sections. The position bounds for each is different, so when I combine the position maps, it gives very funky results in Substance. Is there a way to somehow trick the baker to use the same min/max spherical bounds? Maybe an inverted sphere that encompasses the entire area of the full object thats only in a high sub folder in the baker?
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To get consistent positions, what you would want to do is load all of the objects into a single baker object, and use the texture sets feature (assuming you have more than one UV layout / texture set) to bake all of the maps in one go. To do this, apply a material per texture set to the relevant low poly areas and enable texture sets.