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Vecs is just a box around the model that the engine uses for the most general of checks.
If you want custom collision (ragdoll, projectiles, etc), you have to make it into the model, by skinning convex boxes to bones with 1.0 weight.
To have custom hitboxes, you have to define their shape and size in the model's qc. Hlmv will generate this for you, and allow you to adjust it.