is it possible to make a transition from the last animation to ragdoll
You can setup ragdoll on a character and set BonesWeight to 0 so it’s disabled and bones will use skeletal animation. Then you can toggle it to 1 to start running physics sim on that skeleton.
More docs: Ragdolls | Flax Documentation
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that is, in general, it is possible to make the skeleton partially ragdoll and partially have the animation I specify
Yes, use BonesWeights map on ragdoll that can specify a weight for each skeleton bone individually (by node name).