Couldn't find any information on this. But from there demo video it seems you can polypaint your colormap directly in zBrush. How do I get the swatches into my palette?
Most of my models are polygrouped so i just color fill each polygroup that needs a separate material and then generate a texture at high poly. If you paint color with a brush use 0 focal on the brush so you get sharp edges.
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I would also be interested in how to use the fbx swatch file in Zbrush though. Could be useful to speed up workflow. http://quixel.se/usermanual/quixelsuite/doku.php?id=ddoswatch
Could you perhaps convert the FBX to OBJ and then import it in to Zbrush? Autodesk FBX converter can do the conversion, have not tried it though.
Would be great if Quixel could make the swatches in OBJ format to.
http://www.polycount.com/forum/showthread.php?p=2232173#post2232173