
A Molecular Near Miss - adenadel
http://isohedral.ca/a-molecular-near-miss/
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whatshisface
> _Going further, I note that the ideal bond length was given to me with just
> two significant digits, suggesting that an error of one part in a billion is
> much smaller than our uncertainty in measuring the “true” bond length in the
> first place._

Bonds are flexible and can hold mechanical stress, so there is only a
"preferred" length, not a guaranteed length.

~~~
dekhn
One of my proudest contributions:
[https://www.ncbi.nlm.nih.gov/pubmed/24265211](https://www.ncbi.nlm.nih.gov/pubmed/24265211)

Protein design and fold prediction was being held back by using fixed
(equilibrium) bond angles in proteins, and if you have enough CPU time, you
can optimize those values (they often end up centering around non-equilibrium
angles for the particular atom types) to get better predictions.

~~~
jcims
Do you happen to know if this is related to what was done with AlphaFold? It
sounded like they moved from fixed values to a probabilistic model but I'm not
sure if bond angles was the property they were measuring.

~~~
dekhn
Great question. I don't know.

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jahenderson777
This touches on something I find fascinating: that in the pure world of
perfect maths there's a lot of near misses, things that nearly work out but
don't quite, but that if we have a world where a bit of error is allowed (our
bendy molecular world, with our limited consciousness) then an enormous host
of possibilities opens up. My personal theory is that this is exactly why we
find ourselves in a reality that is slightly fuzzy with an awareness that's
alright but not perfect.

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andybak
For anyone interested in polyhedra I'd like to highlight the wonderful
antiprism project:

[http://www.antiprism.com/](http://www.antiprism.com/)

And the web-based Polyhedronisme for a quick fix:
[http://levskaya.github.io/polyhedronisme/](http://levskaya.github.io/polyhedronisme/)

Finally (personal plug) I've been scratching my own polyhedral itch with a
project that aims to cover similar ground but in a more interactive, visual
way:

[https://github.com/IxxyXR/Polyhydra](https://github.com/IxxyXR/Polyhydra)

(Example output:
[https://photos.google.com/album/AF1QipM029IxQ5P5FacaGywBPlxS...](https://photos.google.com/album/AF1QipM029IxQ5P5FacaGywBPlxSLFFCtyCAXiWXX9p8)
)

One factor that unifies all three projects is conway operations discovered
John "Game of Life" Conway:
[https://en.wikipedia.org/wiki/Conway_polyhedron_notation](https://en.wikipedia.org/wiki/Conway_polyhedron_notation)
later investigated and expanded upon by George Hart - who is mentioned in the
opening of the main article.

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the8472
The linked nature article.

[https://sci-hub.tw/10.1038/s41586-019-1185-4](https://sci-
hub.tw/10.1038/s41586-019-1185-4)

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eljost
Actual atoms in molecules also vibrate all the time, so the provided bond
length he talked about should be seen as an equilibrium bond length.

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beautifulfreak
A graphic illustration of the molecule is here
[https://www.nature.com/articles/s41586-019-1185-4/figures/8](https://www.nature.com/articles/s41586-019-1185-4/figures/8)

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PaulHoule
Reminds me of the time I made a very regular looking polyhedral model that
wasnt and had the hardest time tracking it down.

