Unleash the power of 3D
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Ah, rigify, I’ve had this issue. Sometimes the bones are set inversely concerning their role when it’s generated.

  1. Go into the armature edit mode.
  2. Select the trouble bone
  3. Under the heeader, go to Armature>Recalculate Roll
  4. Choose one, like Local+X

Then after that, edit the weights if you need to.

  1. To do that, first go into the Armature pose mode
  2. Then select the trouble bone
  3. Then select the mesh with the armarture skin weights
  4. Go to Weight paint mode
  5. Now the weight of that bone will show.
  6. Now with that, use the weight painting tools in the toolshelf to smooth it out, make it smaller or larger, etc. There are some great icon tools like “Smooth” and “Limit” and others that really help.

Sometime the upvector of a knee/shoulder/elbow constraint also won’t inverse in generation from rigify, so if after the above doesn’t work – check the rig constraints and drivers on the troubled bone.