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Honestly Matt, you are far more accomplished and knowledgeable than I read in your 1st post. Have really enjoyed all of the responses so far and helpful insights. It just seems sometimes that no matter how much care and attention you put into your work with virtual articulator, surprises happen, just sucks sometimes. So many variables involved, quality of scan which may Look OK?????, import and manipulation. We had a case today for a bite splint, not ios and Man you couldn't find a true centric at all by hand. Dr. Took an open bite record without an anterior stop of any fashion, how is that remotely possible. Squirt in a bunch of pvs and close, but not close, anywhere -impossible! Was wider open in the molar region ×3 compared to the anteriors.you'll want to use Correct antagonist and create overclosing in a uniform way, along the wear facets that exist, and then let the Articulator open those intrusions. if they are uniform, the act of opening should bring the scans to the correct bite. if the intrusions are not uniform, the bite will appear very open.
exocad's approach to this is either to give you a truly vertical opening by shifting everything along the Z or by using the theoretical patient approximation of the articulator hinge to open the jaws, which is why i suggested this to begin with.
however what you can then do is save the new relationship by exporting the scene as one stl or object file before proceeding with any design; once done, you can use this as the bite scan instead, and when aligned with the bite scan, it doesnt matter what the articulator does, they will spring back to the same spot everytime.
you can also use 3rd party software like blender, meshmixer, meshlab, etc, to re-orient and realign data. that lab's skill with mesh work probably stems from some years of familiarity with the digital space so i'm not sure what tools they'd use because everyone's bag of tricks varies; i've given you what i'd do in exocad. this is usually good enough to create jaw relationships with better centric relation and when push comes to shove there's always your software support who should be experienced enough to help you no matter what the problem is. over the years the go-to-answer for any product question of "what do i buy" has always culminated in "the product with the best support" usually for exactly these reasons.
Been at this a while, trust in the Lucia Jig method, 3 bite records in which 2 of 3 must agree. This digital path is so far away from that approach its not even comparable. I do believe however that some excellent tools in digital may be nearer than farther away. That's my hope.
As far as correcting bite and distance from antagonist, its mainly a reflection from feedback from clients. Some need more, some less. Also as ps2thtec said there's no periodontal ligaments in any of our models, quality of provisionals is another concern. I always check my proximal contacts with shimstock, adjust until it pulls through without tearing. Had a new client experiencing proximal contact problems and I suggested they use this standard with the shimstock and bingo we're now having excellent results.
Lots to learn and experiment with, great topic Matt, hope it keeps on going