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If I understand what you are asking, you can do full image metal/roughness just by setting those values and not use a material map sprite.  When the material map sprite is assigned to the same sprite_index (i.e., left as default) then the shaders will draw metal/roughness using the current sprite_index and all pixels at the metal/roughness set.

Yes, that is what I intended to ask. For some reason doing this (setting to sprite_index) does not draw the metal/roughness set the same.  I may need to tinker with the specific metal/roughness settings in light of a change away from the original material sprites.

Ah, it wont be the same with sprite_index because it sets the full sprite to the single value only for metal/roughness.  The actual sprite colors would come out really weird as metal/roughness.  It is possible to try and edit shaders and use like grayscale values, but it will still be a bit odd I think.  The material packer that comes with is your best bet at easily making materials for sprites/pixel art, as most workflows for materials are much more in-depth and require full tools for doing so.

so the material map I was using was a single color. But switching to sprite index, and using the set metallic/smoothness functions doesn’t replicate the lighting effects. I think I I just need to adjust the values to recreate the effect. 

Do you have normal maps also assigned?

Yep. 

Since I have multiple sprites that change depending on the player input, everytime the sprite changes, I get the sprite name and add an "_n" then use asset get index to change the normal map to the sprite that is named the same as sprite index with a "_n" after it. I did notice that when I updated the material map in this way (instead of just setting it to sprite index in the variable defs) the result was much closer to the original set up I had with material sprites, but it wasn't exact. I might be able to tweak the metalic/roughness set numbers to get it to where it was.