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I have designed skins, and a recent version of them involved the use of transparencies to make parts of the skin part of the skin visible under the armor layer. However, when I opened the skin in Minecraft, the transparent blocks became fully opaque, ruining some parts of the skin. I did also notice that some hand-picked colors (used to give a better color difference than the skindex could give) did not show in the skin when making gradients. I built most of the skin in skindex, but the transparencies were made in MC skins 3D.
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Yeah,had this problem too but there's nothing much you can do about it but if you're gonna use the skin for a MC animation,the transparency works and makes the skin a lot better.
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It's likely that there is a smidgen of color left on the parts you erased. You might want to open the file in GIMP or another free editing software and erase transparent parts manually. If there's any color at all it will show as fully opaque because for some reason Minecraft has this all-or-nothing "policy" when it comes to textures.
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Oh. I created a fully opaque version before the transparency version, so I simply reverted to that.