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I want to create geometry with multiple (at least 2) UV maps. One of them will be used to map the base texture (from a texture atlas) and the other one will map a pre-baked lightmap.

I want to export the mesh including both UV maps to a PLY file.

In Blender, I added two UV maps and edited one of them to make them distinguishable:

multiple UV maps

Unfortunately, only the specific UV map marked as "active for rendering" is exported into the PLY file:

[...]
property float x
property float y
property float z
property float nx
property float ny
property float nz
property float s // u
property float t // v
[...]

As PLY allows arbitrary vertex properties, it is not limited to only one pair of texture coordinates per vertex.

Am I missing something or is this a limitation of Blender's PLY exporter?

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This is a limitation in Blender's exporter, but also in the PLY format & its conventional use - which is to only have one UV layer.

You could of course modify the exporter to write shape-keys, weights or any arbitrary vertex data, but other applications won't read it unless special support is added.

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