> once you're used to it, the simple isosurface mesh is super easy to work with
One wouldn't know it from the state of content, or even of much education research, but educational representation is much harder than professional. Students are unable to untangle features reflecting careful correctness, from artistic license. So both seed mis/conceptions. Professionals can downregulate misconceptions... though that can be surprisingly localized - asking first-tier astronomy graduate students "What color is the Sun?"... gets you a common misconception.
Consider that ball-and-stick wrapped with electron density in Fig 9. Imagine coming at it cold. What is that stick? Well, maybe it's a ridge in electron density, thus symbolizing the surrounding not-so-stick-shaped region of increased density which constitutes a bond. But then what are those balls? They're way too similarly sized to be electron density. Ok, maybe they're spherical crosshairs for nucleus location, and the stick is a linear crosshair for the ridge. Variously sized because... something. Oh, no, some of the sticks are doubled, and density certainly doesn't have two ridges, or (here) increased density. So we've a paper notation that badly misrepresents actual electron distribution, blended into a physical representation with a... my head hurts.
I saw a professional chem ed content discussion yesterday, around a misconception, that in a two-species ionic solid, one atom bonds to another, in pairs. Rather than to "4 to 6" neighboring atoms... because one common printed diagram draws 4 neighbors, and another 6. It was like they were non-scientists, thinking they could wordsmith their way to correctness, without the slightest need to examine the actual characteristics of the real physical systems being described, or to consult with someone deeply familiar with them. The focus remained on models, decoupled from reality. I see a lot of that.
Chemistry education research describes chemistry education content using adjectives like "incoherent". Maybe XR can serve as an excuse to do better?
All I can offer in response is vague, hand-wavy speculation about human perceptive and cognitive limitations and how this impacts scientific representations. Coming from a biology background, I'm very used to artistic license and gross oversimplifications - and from years of habit, it almost hurts my brain to think about molecules as anything other than chicken-wire! From your complaint about those representations, I'm guessing you're unfamiliar with "Richardson ribbons": https://en.wikipedia.org/wiki/Ribbon_diagram
Even the developers of these visualizations would probably agree that it's dangerous to rely on them too much, and they are only a way to convey specific information in a way our eyes and brain can quickly process. Crystallographers in particular tended to over-rely on those chicken wire views and that plus software limitations yielded a lot of very poor-quality structures with poor atomic packing. The developer of those ribbon diagrams (Jane Richardson) has done a lot of other work to educate the field about how to visualize packing and other molecular properties and avoid screwing up the analysis. Over the long term, I think constant self-criticism makes up for the occasional sloppiness in scientific research.
My own focus is more on science education representations. And on how badly they describe the represented physical systems. Emphasizing that this seems as much a science community failure, as an education community fail.
Consider an illustration of the solar system in some introductory astronomy content. Let say, that not atypically, it misrepresents sizes, positions, orientations, lighting, and Sun color. Thus creating and reinforcing misconceptions known to be a problem in K-12, in undergrad, and even on into astronomy graduate school. In contrast, consider a line representing an Earth-Mars transfer orbit. It seems unlikely that students will say think there's a material long pole there, and worry about it hitting satellites and cities. Students and teachers are both clear on the aphysicality of the line, but not of the Sun color. Hmm, though using a minimum-energy line to represent an energy landscape is a source of misconceptions.
Similarly, common representation of atoms and molecules are known to be causatively associated with the stew of misconceptions that pervade students and teachers of chemistry. Ribbons, perhaps not so much. Hmm, though also similarly, they're often used without indication of regional flexibility, and so perhaps contribute to the underappreciation of configuration landscapes, of the importance of tuned floppiness. Perhaps.
Consider a currently implausible goal, of science education which accessibly describes the physical world, and conveys a transferable understanding of it. Arguably its content would look much more like scientific visualizations than content does at present. But being for education, it faces additional constraints, challenges and tradeoffs, distinct from those of professional scientific visualization. Creating such would require a collaboration of both deep scientific and educational expertise. For which very little incentive exists at present.
I'm trying to come up with an XR-compatible visual representation of electron density, that is physically correct, accessible, and bears in mind patterns of misconceptions in chemistry education. That task should probably be more than one random software dev's lockdown hobby hack. But as far as I know, that's were we're at. The related NSF-funded work I've seen... doing this bit well wasn't their focus. Same with XR ed tech side. Same with chem ed apps. And scientific visualization programs. And chem ed research. There may well be something nice out there, but I've not yet seen it. And big ed side... I was chatting with a leading textbook publisher, which onboards content creators with the indoctrination that their liberal arts background, and complete unfamiliarity with science and tech, is not a problem... because there's "a scientist" on call. Deriving electron density, with current nice python libraries, and GPUs, has surely gotten vastly easier than it was with old fortran messes, but still... it seems something more is needed here. Some societal staffing seems missing. No?
> once you're used to it, the simple isosurface mesh is super easy to work with
One wouldn't know it from the state of content, or even of much education research, but educational representation is much harder than professional. Students are unable to untangle features reflecting careful correctness, from artistic license. So both seed mis/conceptions. Professionals can downregulate misconceptions... though that can be surprisingly localized - asking first-tier astronomy graduate students "What color is the Sun?"... gets you a common misconception.
Consider that ball-and-stick wrapped with electron density in Fig 9. Imagine coming at it cold. What is that stick? Well, maybe it's a ridge in electron density, thus symbolizing the surrounding not-so-stick-shaped region of increased density which constitutes a bond. But then what are those balls? They're way too similarly sized to be electron density. Ok, maybe they're spherical crosshairs for nucleus location, and the stick is a linear crosshair for the ridge. Variously sized because... something. Oh, no, some of the sticks are doubled, and density certainly doesn't have two ridges, or (here) increased density. So we've a paper notation that badly misrepresents actual electron distribution, blended into a physical representation with a... my head hurts.
I saw a professional chem ed content discussion yesterday, around a misconception, that in a two-species ionic solid, one atom bonds to another, in pairs. Rather than to "4 to 6" neighboring atoms... because one common printed diagram draws 4 neighbors, and another 6. It was like they were non-scientists, thinking they could wordsmith their way to correctness, without the slightest need to examine the actual characteristics of the real physical systems being described, or to consult with someone deeply familiar with them. The focus remained on models, decoupled from reality. I see a lot of that.
Chemistry education research describes chemistry education content using adjectives like "incoherent". Maybe XR can serve as an excuse to do better?