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I do not mean, "How can we see an atom?". I've read those STM microscopes, etc. When I open a textbook on an atom it shows a structure. When I look at something more complex like a Crystal, the structure is shown something like this video,

https://youtu.be/v1enr8PIMOw?t=202

or this model,

https://www.amazon.com/Molecular-Models-Company-14-Quartz722-Structure/dp/B00LEFE03S

Do we really know they look like that or are those physical representations of mathematical representations and what we think they must look like? Is this simply the way we envision they'd have to look like or might look like?

johnny
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    This question might be better suited to [Chemistry.SE], or perhaps even [Philosophy.SE]. – Michael Seifert Dec 18 '20 at 15:04
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    @MichaelSeifert I am surprised. Now Physics does not deal with atoms anymore? – GiorgioP-DoomsdayClockIsAt-90 Dec 18 '20 at 15:51
  • @GiorgioP sure, but then at what point do we draw the line at chemistry since everything could boil down to physics? At some point it's just easier to appeal to the larger chemistry explanation than using physics in everything – Triatticus Dec 18 '20 at 23:02
  • @Triatticus why should we draw a line? It is a fact that in departments and research centers physicists and chemists work on atomic systems and molecules attaching the same problems with the same techniques. In my opinion, this is the best evidence of a continuous transition between Physics and Chemistry without a discontinuous border. At least in this sector of the research. – GiorgioP-DoomsdayClockIsAt-90 Dec 19 '20 at 07:17

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There are no colors, there are no sticks. Many of these models are not meant to show what molecules might look like "in reality".

STM and especially AFM (atomic force microscopes) show how surfaces of crystal structures would "feel" like.

Computations of electron density isosurfaces or of the MEP (molecular electrostatic potential) are reasonably representative of what molecules would feel like.

Here a computed isosurface (by Itamblyn), a surface inside and a surface outside, and a conventional molecular model between those to help with interpretation.

C60 isosurface

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Understanding visualization conventions of atomic and molecular structures is an important piece of knowledge for a physicist. I stress the word conventions. All the ways we can access or measure atomic positions are not directly based on visible light. People have elaborated many different visualization conventions. All of them provide visual information about the positions or equilibrium positions of the atoms. Moreover, additional information is encoded into diameters of spheres, colors, sticks (distances and/or kind of bond), isosurfaces, clouds etc.

It is important to bear in mind that all these conventions are just ways of encoding physical properties into visual elements. They do not have any real existence.

GiorgioP-DoomsdayClockIsAt-90
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  • As a laymen, it sounded like they take "topographical" (only word I know to use) measurements and construct something, but the traditional models weren't based on anything in our present technology, so did we keep the visible structures based on tradition? Were the 3d measurements taken and displayed in a way to fit that presupposed structure (like the image in the original question)? – johnny Dec 18 '20 at 18:23
  • @johnny Exact 3d positions often come from x-ray diffraction, which can also produce maps of the electron density. Some sticks (like those in models of NaCl) are purely conventional, others are reasonable representations of chemical bonds. –  Dec 18 '20 at 18:29
  • Thanks. They always make it look like they know for sure x molecule or atom looks like x, but they are representations. The science behind them is solid because we can test things and observe, but the visual is to help us understand things. It seems so anyway. – johnny Dec 18 '20 at 18:33