# Realistic molecular modeling? **URL:** \ **Category:** Factual Questions\ **Created:** [February 8, 2009, 6:28pm UTC](https://boards.straightdope.com/t/realistic-molecular-modeling/484942 "2009-02-08T18:28:55Z")\ **Posts on this page:** 5\ **Page:** 2
**Author:** ![Anaglyph](https://avatars.discourse-cdn.com/v4/letter/a/ed8c4c/32.png) [@Anaglyph](https://boards.straightdope.com/u/Anaglyph)\ **Post date:** [February 9, 2009, 2:33pm UTC](https://boards.straightdope.com/t/realistic-molecular-modeling/484942/21 "2009-02-09T14:33:23Z")
> [@WarmNPrickly](#): > > Technically this is true, but of course the only reason this works is because you have a large repeating unit. You aren’t really looking at individual molecules. Also, you can’t really see protons with x-ray crystallography. Usually the position of the proton is just guessed at by the crystallographer. Neutron scattering can pick out protons. Structures of complex molecules such as protiens have additional difficulties in that they rarely crystalize out in the same form they are in solution. There are two reasons why we need large repeating units in x-ray crystallography: - We do not really have good enough X-ray optics to focus an X-ray image - X-rays are too energetic and therefore will destroy a single molecule before enough photons have interacted to form a detailed picture of that molecule. ---
**Author:** ![Solfy](https://avatars.discourse-cdn.com/v4/letter/s/848f3c/32.png) [@Solfy](https://boards.straightdope.com/u/Solfy)\ **Post date:** [February 9, 2009, 2:43pm UTC](https://boards.straightdope.com/t/realistic-molecular-modeling/484942/22 "2009-02-09T14:43:43Z")
> [@mangeorge](#): > > I work at the research facility for a huge multi-national oil company. We have labs inhabited by a few scientists, lotsa chemists, and a mob of lab rats. They like to display these models, and they are the stick-and-ball variety shown in the linked article. > That’s what spurred my curiosity. > Chemistry people are an odd lot. I asked one of them what that is, and she said “it’s a molecule”. I then asked “is that what one actually looks like?” and she had a giggle fit. > Sounds familiar, doesn’t it. Maybe she thinks I’m cute. :dubious: She sure is. The stick and ball models are a handy way of understanding how a molecule behaves. For example, certain balls of a particular model are carbon and they have four sticks poking out of them, they can make four bonds with particular angles and lengths. When you stick them to other carbon balls, fun shapes start to appear. Chemists use these models to undestand the shapes of the molecules, which help us understand and predict physical and chemical properties. They don’t mean much in terms of “what does the molecule really look like,” but they are handy in figuring out how a molecule might act, and how we might manipulate it. In this way, organic chemistry can be thought of as building with \*really \*tiny Legos. As for whether she thinks you’re cute, well, she might have been huffing solvents. . . ---
**Author:** ![mangeorge](https://avatars.discourse-cdn.com/v4/letter/m/d78d45/32.png) [@mangeorge](https://boards.straightdope.com/u/mangeorge)\ **Post date:** [February 9, 2009, 3:26pm UTC](https://boards.straightdope.com/t/realistic-molecular-modeling/484942/23 "2009-02-09T15:26:55Z")
> [@Solfy](#): > > As for whether she thinks you’re cute, well, she might have been huffing solvents. . . Go ahead, destroy this old man’s ego. ---
**Author:** ![Napier](https://avatars.discourse-cdn.com/v4/letter/n/ce73a5/32.png) [@Napier](https://boards.straightdope.com/u/Napier)\ **Post date:** [February 10, 2009, 2:57am UTC](https://boards.straightdope.com/t/realistic-molecular-modeling/484942/24 "2009-02-10T02:57:25Z")
There are two kinds of stick and ball molecular models. One has balls that are no more than maybe 20% as big as the ball-to-ball separations are. The other (I think it’s called “space filling”) has balls big enough and separations small enough that the balls have to have flattened spots where they join together. If you could feel molecule shapes with your hands, or have an atomic force microscope to do it for you, you’d find that the space filling type of modeling kit would be much more like the true shape. I played with a desktop AFM about 10 or so years ago. A friend and I went to a seller of such things in New Jersey and had a pleasant afternoon of it. To look at the things, you wouldn’t think they were going to take you where they take you. This company was promoting “personal AFM” for every desktop at a price around $20,000. ---
**Author:** ![beowulff](https://sea3.discourse-cdn.com/straightdope/user_avatar/boards.straightdope.com/beowulff/32/542_2.png) [@beowulff](https://boards.straightdope.com/u/beowulff)\ **Post date:** [February 10, 2009, 4:53am UTC](https://boards.straightdope.com/t/realistic-molecular-modeling/484942/25 "2009-02-10T04:53:58Z")
Check these out: [Molecular Visualization Freeware](http://www.umass.edu/microbio/rasmol/) [Previous page](https://boards.straightdope.com/t/realistic-molecular-modeling/484942.md?page=1)