I think this would help a lot to save time needed to produce images, reduce internet traffic and make understanding of the structures easier, if only there would be a better way rather than putting a static image of a 3D structure.

How can one use JSmol or similar tools to achieve such interactivity on ChemSE?


1 Answer 1


Although I up-voted your request, because I like the idea of making structures more accessible to the general user base, I would still need some really good convincing that this was necessary, and which cases would actually benefit from it. I personally dislike JSmol and other embedded interactive elements, because from my experience they drastically increase load times for a web site. We all know that even MathJax can be a real nuisance. Adding on to that is probably a bad idea.

The other concern I have is, how platform independent such an embedded element is. If not everyone can use it, then it is not beneficial at all. Again, we have seen that some posts with MathJax simply don't work (don't render) with the apps because of missing support (the used version is far behind). I tried JSmol on my android phone, which works surprisingly well, but it took long enough to load that I would loose interest in the post.

In my opinion, if we would introduce such a feature, it needs to be in addition to a still frame, and you must actively engage in order to load it. In any other case I assume it would just over complicate the site.
On occasion I have used animated gif to show rotations or certain angles of a molecule. This is because on the internet that is easier to make a point. However, if I were to publish similar results/explanations in a journal I would choose a different mode of presentation.

There are a variety of online tools that allow linking to such structures, so feel free to include external sources in your post. For example: Have a look at this fabulous structure of benzoic acid.

Lastly, I certainly would hope that a way to draw structural formulae on the site is going to be introduced before molecular structures. And we all know, this is already a long shot. We have talked about it (on and off) since the beginning of the site, without any significant change in status quo. (We don't even know if it is being considered.)

  • $\begingroup$ Although I accepted your answer... Just kidding. Yeah, Java applets were horrible 10 years ago, and if they still would be around, they would remain horrible. JavaScript though had a bad start, but these days all computers and smartphones play along with JS pretty nicely. Usually one requires to draw more than one picture with a reasonably high DPI which results in about 200-500 Kb each, adding up to 2 to 5 Mb in case of complex structures where you might want to show a lot of stuff. JSmol loads once, and can pick 5 kB CIFs on the fly allowing for great flexibility. $\endgroup$
    – andselisk Mod
    Jun 27, 2017 at 7:57
  • $\begingroup$ Also, I think data production rate these days increases in geometrical progression, and "releasing" publication model will soon become obsolete, in favor of "rolling" data exchange, when static images or PDFs representing datasets (such as XRD experiments) are no longer will be viable. "If you want to make enemies, try to change something", I know, but I have a feeling that at some point changes must occur. $\endgroup$
    – andselisk Mod
    Jun 27, 2017 at 8:06

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