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Advanced Skeleton Building Problem

SuperSparkplug
polycounter lvl 9
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SuperSparkplug polycounter lvl 9
A friend of mine recently recommended I use Advanced Skeleton for rigging a character I want to animate. I looked up a tutorial and followed it but I'm having several problems. I'm not sure if everyone here is familiar with Advanced Skeleton, but it seems to be pretty popular, so I hope someone knows.

First off, I know that Advanced Skeleton prefers that you rotate a joint and only move it in Translate X, however this becomes a huge issue when the hand is involved since there are not enough joints to support robust rotation in that area without ruining the alignment in that area. Furthermore, the only way to get them to align properly is to move them in any axis possible since the joints are far too spread out.

Secondly, every time I select my root joint and tell Advanced Skeleton to build itself, several joints, always the figures and sometimes the legs, completely misalign themselves with how I set them and builds the skeleton according to that misalignment. The fingers become the biggest problem for this reason because now they no longer match up with my rig. No amount of using the Toggle Fit/Advanced function to go back and fix it for rebuilding seems to solve this.

Does anyone know what the problem is here?

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