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That's right, I have two broken bones now. The proximal bone is fixed, and the distal bone is reduced. Then, I divide the reduction steps into many relative pose matrices (including rotation angle and translation component), each representing a matrix.How to create a Mot file for two broken bones with their own coordinate systems?

Hello,

Motion files contain the time history of coordinates. If you want a motion file to represent bone fracture reduction then you should introduce a joint into the model between the two broken bones with corresponding coordinate(s) such that you produce the motion by changing coordinate values, place these coordinate values in a motion file then play it.
If all what you want is an animation rather than a physics based simulation, this may be an overkill but it's your call.

Hope this helps,
-Ayman