Talk:Molecular graphics

Chemistry Mid‑importance

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Connolly Surface ≠ Isosurface[edit]

The commonest isosurfaces are the Connolly surface, or the volume within which a given proportion of the electron density lies.

A Connolly surface ("molecular surface", or "solvent-excluded surface") is based on a spherical probe's reach into a group of atoms, with each atom defined by vdW radii. This is not the same thing as a level set of electron density. It's a kind of approximation, sure, but not one in which tweaking of parameters (probe radius, vdW radii) would result in convergence on any actual isosurface.

Wait, I take that back. If you define your electron density as a specific, distinct value at the surfaces described by vdW radii, but also distinct from the surface portions within other atoms, (thus basically designating a CPK surface as a distinct, contiguous, single-value set) then a probe radius of zero would get you that isosurface. In short, that's silly.

The Connolly surface, if I understand correctly, even excludes cavities. You just can't stick your probe in there, my friend. But my real issue here is that the surface of the probe is not delineating a level set, it's specifically defining something else — solvent exclusion.

We might say "The commonest isosurface is a very rough and unintentional approximation of one, called the Connolly surface, representing electron density" if we actually want to consider the Connolly surface to be an isosurface.

—63.249.110.34 (talk) 09:59, 18 March 2009 (UTC)[reply]

I agree with your analysis - I used "isosurface" loosely and - as with any WP article you should go ahead and rewrite bits. 82.6.101.105 (talk) 21:24, 6 April 2009 (UTC) Petermr (talk) 21:25, 6 April 2009 (UTC)[reply]

Alrighty, see if that looks any better. —Raymond Keller (talk) 07:31, 18 March 2010 (UTC)[reply]

Speaking of isosurfaces, where on earth is Figure 5, referred to in the last paragraph of the Space-filling models section?

Refimprove[edit]

It is surprising (and somewhat disappointing) that this article has been around as long as it has, and has reached the depth that it has, on the strength of only two references. There are whole sections that are based, as far as I can tell, on original research or personal experience. WikiDan61^ChatMe!_ReadMe!! 18:50, 18 June 2009 (UTC)[reply]

somebody screwed up[edit]

It says, "The isosurface in Fig. 5 appears to show the electrostatic potential," but there is no Fig. 5. Verdana♥Bold 08:11, 22 July 2020 (UTC)[reply]

Philosophy?[edit]

Does that mean it isn't a science? It can't be both a philosophy and a science as they are antithetical. It should be classed under pseudoscience in that case. Calling it the art of graphical representation of molecules would be one solution. --ෆාට් බුබුල (talk) 08:24, 4 November 2022 (UTC)[reply]