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I have two bones. When i go in to pose mode an select each of them respectively, i can see that they have different coordinate systems / rotation matrices. How do i make them have the same Coordinate system / rotation matrix? So the x-, y-, and z-axis is the same for each bone?

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First select the bones you want to have the same coordinate system, make sure that the Active bone is the one rotation matrix you want to give to the other, now press CtrlN to open the 'Recalculate Roll' properties and choose Active Bone.

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