I don't use fragmotion only to get stubborn xfile into a format I can deal with and get the animations.
I am not saying I love it, but I can bet that 3/4 of the weapons made for classic FPSC were made in this program.
I use 3d max myself.
I can rig this for you, But I am betting that BSP user has a real good handle on this stuff for reloaded. Send me a PM or email me below, and we can discuss your needs.
Check out his post if you have not already. He is a nice guy and would probably answer your questions on the most efficient way of doing this.
Once you have the first rig, switching weapons and changing animation is faster and easier.
I have not messed with blender since it got animation export capabilities, so I cant help you there, sorry
And I agree with Wolf completely, there is a chain of programs for free and pay that each has its specialty that works best for direct x format. I have learned over the years that I may not like a 5 program workflow, but that is what is needed sometimes, to get the dream in your head to the game engine.
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