Scaling models
You can scale the model by scaling the empty (root object).
credit: Kizuna AI by Project A.I.
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Export PMX as FBX for Clip Studio Modeler
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Convert the material to Blender, and export FBX with these options:
How to setup physics
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You should setup physics in PmxEditor, because changing values is easier.
How to convert to MMD material
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If your material is using BSDF nodes or Emission, you can convert them into MMD shader (MMDShaderDev).
How to add transparency to material
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Adjust MMD Material > Alpha to add transparency.