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> computer generated imagery to define the “surface” of an atom The grids are isosurfaces of electron density. Analogous to isolines on a map illustrating mo

> computer generated imagery to define the “surface” of an atom The grids are isosurfaces of electron density. Analogous to isolines on a map illustrating mountain terrain height. Atoms are sticky little fuzzy balls. The fuzz, electron density, falls off exponentially. They don't have an "edge" in a non-fuzzy-object sense. Analogous to a stereotype volcano having an arbitrary perimeter. Where would I place it? Where you need climbing gear? Where biking up gets hard? In the foothills? Somewhere on the sloped plain? You place the perimeter wherever is convenient for what you're trying to use it for. People are usually interested in the densities between sticking atoms, which are several orders of magnitude down from peak density. Analogous to drawing an isoline at "the towering volcano is here high enough to start stubbing your toe on it". The picture draws isosurfaces of electron density at something like "around here one atom would 'bump' another, and you can see bonds" and at "I wrap a single atom only, but still have an interesting shape". To show the various features of interest, one draws multiple isosurfaces. As with a terrain map. But an exponential electron density scale is harder to represent than linear height scale. And it's hard to clearly draw more than a couple of nested 3D isosurfaces. So instead of placing many iso's at linear steps, here there are just a couple, more like an order of magnitude apart.

natechols 6y ago
The terrain analogy is great - this is how the first structural biologists had to view electron density: https://image.slideserve.com/105608/electron-density-maps-of-proteins-sperm-whale-myoglobin-2-4-angstrom-resolution-l.jpg https://image.slideserve.com/105608/electron-density-maps-of... I think this is a stack of 2d "slices" through the density, printed on transparencies. But I've also seen 2d representations of charge density (some of which is just theoretical studies) that are even more similar to a terrain map.
- mncharity 6y ago
  Neat. I've been exploring visual representations of electron density, optimized for educational use with XR. Intending to illustrate that science education content could be made transformatively less wretched. Isosurfaces and nonlinear color gradients are educationally problematic. And fuzz gradients are hard to visually stereo fuse. And on near-term AR displays, black is transparent, and background environment colors can't be manipulated, which limits the space of attainable colorizations. My current thought is to approach it as a volumetric light source. Composed of several linear scales, each a different color, with density as transparency. And respecting their true density when combined, so higher density scales "shine through" lower. We'll see. Maybe overlay random sample "sparkles" to maybe improve sense of spatial extent. I've not seen much similar work. If you know of any, I'd love to hear of it. Also, it seems there was a push some years back to emphasize electron density when teaching intro chemistry. A push that doesn't seem to have gelled. I've guesses, but I'd value thoughts on why.
  - natechols 6y ago
    I've been out of the field for a few years, but I know that the graphics hardware (and accompanying software tools) make what you're describing much easier. This is best example I can come up with: https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-4-17 https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-29... (see page 12) Random asides: 1. once you're used to it, the simple isosurface mesh is super easy to work with (i.e. build molecules into), and for structural biologists the broad approximation is perfectly adequate 2. even so, the amount of unexplained blobs - some of which are definitely not noise - in my (xray) electron density maps was always both fascinating and frustrating. that's one reason why we don't spend much time on fancy renderings of experimental density at anything worse than subatomic resolution, because you're just sharpening the features that your atomic model doesn't explain.
    - mncharity 6y ago
      Thank you. > 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?

natechols 6y ago

The terrain analogy is great - this is how the first structural biologists had to view electron density: https://image.slideserve.com/105608/electron-density-maps-of-proteins-sperm-whale-myoglobin-2-4-angstrom-resolution-l.jpg https://image.slideserve.com/105608/electron-density-maps-of... I think this is a stack of 2d "slices" through the density, printed on transparencies. But I've also seen 2d representations of charge density (some of which is just theoretical studies) that are even more similar to a terrain map.

mncharity 6y ago
Neat. I've been exploring visual representations of electron density, optimized for educational use with XR. Intending to illustrate that science education content could be made transformatively less wretched. Isosurfaces and nonlinear color gradients are educationally problematic. And fuzz gradients are hard to visually stereo fuse. And on near-term AR displays, black is transparent, and background environment colors can't be manipulated, which limits the space of attainable colorizations. My current thought is to approach it as a volumetric light source. Composed of several linear scales, each a different color, with density as transparency. And respecting their true density when combined, so higher density scales "shine through" lower. We'll see. Maybe overlay random sample "sparkles" to maybe improve sense of spatial extent. I've not seen much similar work. If you know of any, I'd love to hear of it. Also, it seems there was a push some years back to emphasize electron density when teaching intro chemistry. A push that doesn't seem to have gelled. I've guesses, but I'd value thoughts on why.
- natechols 6y ago
  I've been out of the field for a few years, but I know that the graphics hardware (and accompanying software tools) make what you're describing much easier. This is best example I can come up with: https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-2946-4-17 https://jcheminf.biomedcentral.com/track/pdf/10.1186/1758-29... (see page 12) Random asides: 1. once you're used to it, the simple isosurface mesh is super easy to work with (i.e. build molecules into), and for structural biologists the broad approximation is perfectly adequate 2. even so, the amount of unexplained blobs - some of which are definitely not noise - in my (xray) electron density maps was always both fascinating and frustrating. that's one reason why we don't spend much time on fancy renderings of experimental density at anything worse than subatomic resolution, because you're just sharpening the features that your atomic model doesn't explain.
  - mncharity 6y ago
    Thank you. > 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?