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I have a humanoid mesh and created a meta rig with rigify. All goes according plan except after skinning the mesh the fingers don't behave as they should when scaling the finger controls (wanting to make a fist), all the fingers go off in a wonky direction some bending upwards or sideways instead of down. So... I figured that I screwed up the rotation of the bones at some point. Is there a good way to go back to the meta rig stage and adjust the rotation of the bones to line up with the mesh better. I feel like I saw this somewhere but now cannot find it.

Edit:

I believe what I'm looking for is a way to automatically adjust the "Roll" of each finger bone to align with the hand. Am I looking at this the correct way?

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When rigging with rigify, most of the time bone roll will be correct, however on occasion if you have to adjust the metarig a lot, the rolls can get distorted. This is particularly common on the fingers as they have many segments and often require a bit of adjustment depending on the exact position that the hand is modeled. I find is always worth checking bone rolls in the hand when using rigify.

Rolls can be adjusted with ctrl-R. For rigify fingers you should have the bone's Z axis pointing in the direction you want the finger to curl when you scale the control bone down. There is no automatic way of setting this as it depends on the mesh.

Re-running generate from the metarig will update the generated rig provided you have not renamed it.

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