There are a lot of bones in the rig and you need to tell Blender which ones will actually deform the meshes. By default, all of them will deform it, so let’s see what you can do to define the specific deformer bones.
On the Bone tab of the Properties Editor, you can find the Deform panel. When it’s enabled, you’ll be able to set up the envelopes (the areas of influence that surround the bones) and some other features of the bone deformations. Now, if you don’t want a particular bone to deform the mesh, then you just need to disable that option for that bone. Of course, doing it for every single bone, one by one, would be very slow, so let’s look at a fast way to do it:
1. In Edit or Pose Mode, select every bone and, with all the layers enabled (all the bones visible), press Shift + W to display the Bone Settings options. Alternatively, you can find those options in the Armature or Pose menus (depending on whether you are in Edit Mode or Pose Mode) on the 3D View header under Bone Settings.
2. In the Bone Settings menu, click the Deform option: now all the bones have been set to not deform the mesh. Deselect everything. Select those bones that you don’t want to deform the mesh and make sure that on the Bone tab, the Deform option is disabled.
3. Now go to the Armature Layers and turn on just the layer for the deform bones. Select all those bones, press Shift + W again, and pick the Deform option a second time. Now those bones have been enabled as deformers, and all the rest (controller and helper bones) are not going to affect the mesh at all.
That was pretty quick, right? Can you see how layers and groups allow you to quickly select and change settings for particular types of bones?
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