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im trying to make a a gecko armature but there's a few things I'm trying to figure out 1. how would i make ball joints that gradually become smaller 2. how would I make hip joints that have a angled shaped  3 how would i connect a breathing plate to the neck 4. what joints i should use for the small tiny legs and how should i connect the head to the body 5. how should i make a sort of clock work head that would be capable of holding a tounge. I made a quick mock up of the armature its a wip but might help with my explanation.

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I think if the plates for the thighs/upper arms are above and below, that will give maximum movement forwards and backwards, with limited movement up and down.

I have done a few crawling lizards, but I used aluminium armature wire for the armatures, so I could make the joints move any way I wanted, and the wire was compact and fit inside the sculpted shape quite easily.

I have only made a breathing plate twice, and it was for an ape and an apelike monster, so it only had to move forward and backwards in the front of the chest.  I had an aluminium block with a smooth hole in it, with a bolt going through that could turn freely in it.  The plate had a smaller block with a threaded hole, so as the bolt turned in place, it moved forward and back.  I shot a video of it when the latex had perished and I was stripping the armature:  

 

Some dino puppet armatures I have seen pics of (by Jim Danforth I think) had 2 sides that moved in and out, which is more complicated.  Can't help with that.

When I do a tongue, it is pretty simple - thin armature wire bent in a zigzag shape, so it can stretch longer or compress shorter.  Then I glue soft foam onto both sides, trim, and dab with liquid latex.  You could sculpt and cast a tongue, but the foam and latex buildup makes a pretty good tongue texture anyway.  I have a hole near the back of the lower jaw to glue the back end of the tongue wire in to attach it.  

they have really weird places where you can see them breathing its like right under the back of the jaw and then right in front of the front legs Crested gecko heavy breathing - YouTube

i was hoping of using mine for the reference tot his but he sadly passed away near the start of the project 

Frogs do that throat breathing thing, too, so I know what you mean.  Maybe something in the head, with a lever that goes back to the throat to push against the skin?  A cam action could work, where you can keep turning the screw in the same direction. I did that for a rocking boat.  The cam was actually a perfect circle but the hole was not in the middle, so it did the same thing as an oval shaped cam only more smoothly.  As it turned it would rub against the keel, and gradually lift the boat, then lower it.  It had a natural ease-in and ease-out as the rocking changed directions.  It was easier there than in your gecko though, it could be out of shot under the boat, it didn't have to be concealed inside a puppet.

Something like this maybe?

Yes that would definitely work

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