Fun you can have with your three year old and protein crystallography/NMR coordinate data.

So basically, I've been hearing stuff about some new game show that pits adults against the sort of knowledge that a child in Grade 5 should know. It sounds like a pretty interesting concept, and has gotten me thinking about kids and science information generally.

Anyway with this in mind, today, I thought we could play around with a piece of free software that enables folks to look at three dimensional structures of a varety of biologically relevant molecules.

Because kids like video games right? And what could be more challenging to young inquiring hands than navigating the structure coordinates of a drug into some docking site found on a protein. Seriously, can't you see this somewhere on level 5 of some Zelda type game?

Anyway, the software I'm referring to is called Cn3D and can be found free to download here. It is a bonafide research tool for things such as the above drug design situation, or simply for researchers to look at a molecule from a three dimensional snese so that they can design mutations, etc. At the very least, it's cool because you can do something akin to "look at the pretty molecule," and, perhaps most importantly it's really easy to use.

There's an online tutorial at the site, but here is an easy five step instruction guide on mucking around with the software tool.

1. The DOWNLOAD THE SOFTWARE step:
Once unstuffed, unzipped etc, the program can act as a stand alone, or you can do some funky preference stuff to make your browser open it up automatically. My son Ben (who is three) had difficulty pronouncing "preferences" (instead saying nefrences?), so we will stick with the software on its own.

2. The SEARCH FOR A STRUCTURE step.
This is actually the confusing part since there happens to be a database of some 40,000 coordinates available for download (what are coordinates? basically math data specifying all the atoms and their spatial relation). You can search the database anywhere on the Cn3D site (at the top), so since Ben at this point only knows how to spell his name, we typed in "BEN." Doing this, we noticed something for "Trypsin after a high dose X Ray 'burn'." Ooh... that sounds cool (Ben agrees).

3. The DOWNLOAD A STRUCTURE step.
Anyway, click on the entry, and then click the "view 3D structure" button. Basically, the browser should begin downloading a file that is more than likely going to be called mmdb.cn3 . If the trypsin example doesn't appeal to you, you can try searching for "IgG antibody" or "deoxyribonucleic acid" for some structures that might look a little familiar.

4. The LAUNCH CN3D PROGRAM AND OPEN THE COORDINATE FILE step
Hence the, "look at the pretty molecule" effect.

5. The MOVE THE MOUSE AROUND AND PRESS BUTTONS INDISCRIMINANTLY step.
Given enough time, even Ben will figure out that these mouse buttons can do a lot of the most basic movement functions (like move the structure, turn the structure, zoom in and out of structure).

Ta da!