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I'm looking at 3D modeling a large bird like an emu or ostrich, but I don't know how the muscles surrounding the femur connect to the hips/back. It seems weird that the entire thigh and quadriceps would be fused into the hip because that would greatly reduce the range of motion of the femur which affects how I animate it, but I can't find any reference that shows it either way.

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This is probably WAAAAY to late to be of any use to you but hey... So the simple answer is: Kinda. You were actually correct to intuit that the femora of birds have a limited range of motion, with most of the limb motion being provided from the "knee"-down. So you shouldn't animate bird legs the same way that you would the legs of other non-bird animals. That's not to say that the femur doesn't move - it does but not my much (it typically doesn't extend posteriorly beyond the vertical). Much of the thicc thigh musculature is there for support.

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