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This is difficult to describe, not sure what it might be called as a post in the forum. I have been dealing with an issue where a single layer (arm) is passing over itself and does not know if the dragger handle should be above or below the layer order of the origin point. This has the effect (as you can see in the video) of the hand disappearing underneath the shoulder. Is there a fix/work around for this that does not wrap the arm unnecessarily? I know other people must be having this problem, how is everyone else addressing it?
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So anything on the same mesh / hierarchy level is going to run into issues like this, z-fighting for the same space. This is why we say make arms and legs independent from the torso (as you have here), so they don't fight for the same space.
You best bet may be creating some kind of independent chain - see Physics Playground at http://adobe.com/go/chexamples - the rag doll guy and wrecking ball chain have several interlinked attached parts that don't fight with each other. I wonder if that problematic white part could be one independent piece and the rest of the arm as another attached part.
I will explore the link to the Physics Playground a little later this afternoon when I work on this project again. I actually started troubleshooting by making the arm independent from the piece of the sleeve that is giving me the runaround, which had a completely separate set of issues, (mainly that the sleeve and arm would not move in tandem.) I'm still getting used to the workflow that does not involve staples. Mostly it is improved, but sometimes I still have issues with independent layers moving away from a point at which they are supposed to connect with the rest of the artwork. I'll post again soon, with updates as to how well I have addressed this issue.
Right now, the most expedient workaround I am using involves making a separate puppet to perform each individual action needed per scene. So I would create a puppet that in this scene has two individual independent layers for his right arm, one from the shoulder to the elbow, and the other from the elbow to the wrist. That way I could preserve the z-axis dynamic that need to be there, but it would be a separate puppet from the one I use for any other action. It's a lot of work, building and rigging a separate puppet for every scene, but it seems to be the only way to get the results I am after...