This completes the uploading of the DNA nucleobase models to Warehouse. To see it, all you have to do is go to Google 3D Warehouse and enter Thymine. I realize that Google primarily intends the Sketchup/Warehouse paradigm for architectural modeling, but it’s still pretty amazing to me that I’m the only person to model basic molecules there.
Based on the Arduino Duemilanova models I found in Google 3D Warehouse. It seems that one Arduino model is based upon another in the Warehouse in an evolutionary growth, so it’s hard to give credit for the original design. Suffice to say, I’ve had to revise and add stuff, but I didn’t start from scratch.
Anyhow, my goal is to show every single jot and tittle on the Arduino board without recourse to phototexturing. Then sometime this month I plan to scale it a thousand fold, set it on a foundation and erect observation platforms and conduct a guided tour . . . it’ll work. Trust me.
Check it out in Google 3D Warehouse here.
I’m going slow on the uploading, for two reasons. First, there’s always a good possibility that there is a fundamental shortcoming in my design which will force me to redo everything. Second, I want to concentrate on other projects now.
Still, my ambition is to upload a hundred molecules.
(UPDATE 1/11/11 [oooh, I just noticed that!]: True to prophetic utterance, I made a mistake and had to omit a double bond in the guanine model that I originally uploaded. This updated version of the blog post is correct, as is the model now resident in Google 3D Warehouse. He Said.)
Kind of overwhelms the images in Warehouse. Have to work on that. But at least I toned it down from this:
That’s what I uploaded. This time I think it will stay. You can visit it in the 3D warehouse by clicking here.
Here is my stupid logo:
Originally, I used the Martian tripod as my logo, then I had second thoughts. What am I trying to represent with that? It didn’t seem to have anything to do with molecules, for sure.
Anyhow, this logo is just a placeholder. I’ll come up with something nicer. I’ve got ideas. I’ve always got ideas.
And my master plan to monopolize the Google 3D Warehouse ball and stick molecular model market will pick up speed now that I’m pretty sure most of the bugs of my molecular maker have been ironed out.
(Now there’s a mixed metaphor that it doesn’t pay to think about!)
A problem with putting the letters on the sides of the icosahedra (yes, that is plural for ‘icosahedron’ according to the WordPress spell checker — which by the way treats ‘WordPress’ as a typo). Where was I? Oh, yes, a problem with putting letters on the sides of the icosahedra. The 3D letters are outlined in black, and from a distance all you can see of the letters are the black outlines, and from an even greater distance all you can see of the faces are the outlines of the black letters, the color of the faces being completely crowded out.
I tried to remedy this by changing the letter color to transparent:
Then I made the letters flat and tried a different font (Calligraph421BT — did you know there was such a thing anywhere, let alone in Sketchup?). And that did look nicer:
It looks nicer still in close-up:
Oooh, this looks so pretty I could see hanging a ‘DNA Mobile’ made of atoms like this! Calligraph421BT, your existence is justified!
As I started to add more atoms to the Sketchup molecule maker kit, I realized that the chemistry model color convention breaks down past the basic four atoms of hydrogen, oxygen, nitrogen, and carbon. Green, for example, is used for both chlorine and phosphorus!
So I thought, what if we label the atoms for better identification? Then I thought it wouldn’t look too cool to do this on a ball, but how about a multi-faceted shape, say a buckyball? Well, that proved impractical, but I did find this nifty icosahedron (twenty-sided) in the Warehouse.
The original was made by Google, but then I modified it so that all the faces are manifestations of one component. Thus if I change one face, I change them all. This makes it easy to create a veritable zoo of atoms!
Plus, it looks cool.
Here is a screen capture of the latest version of Molecule Maker. Notice the scene tabs, which facilitate zooming in and out. I had to de-select scene transitions to make it work smoother (which, I admit, seems counterintuitive).
The lines sticking out of everything are ‘scaffolding,’ a little trick I learned in Sketchup to align groups and components together. The scaffolding lines are part of a component, and once no longer needed, can be universally deleted with a few clicks of thine mouse.
So how well does the new improved and expanded Molecule Maker work? Not as well as I’d hoped. I had hoped that it would be orders of magnitude faster than the simple version, but it’s only about twice as fast. And you know, I think a physical model set would be twice as fast yet.
I expect to add some methyl group examples, and I need balls for phosphorus, iron, etc. And I think the pentagon-hexagon ‘snowman’ and related templates need to be tilted sideways, to recognize that the work space is wider than high.
My ambition — I’m not sure I want to call it a goal yet — is to do a hundred molecules and upload them to Google 3D Warehouse. That could easily be done within a month, or if I dally, a year. Because my ADD is telling me it’s about time to be distracted.
Well, I was right about being wrong. Here is adenine with the correct angles for the hydrogen bonds coming off the pentagonal ring:
And here is the molecule maker kit, admittedly not looking like much for something that has kept me busy for so many days now but that is the way it works sometimes:
Uracil is really easy to make. All you have to do is get rid of the ‘antlers’ of the methyl group on thymine and replace with a ‘unicorn horn’ of hydrogen for uracil. Actually, scientists believe the evolutionary path was in the other direction, from Uracil in RNA to Thymine in DNA, like so:
Why did this evolutionary transition occur? My scientific theory is that originally, briefly, during the course of evolutionary history, there was a version of DNA with uracil, but one day the methyl fairy came along and blessed it, and that’s how thymine got its antlers. The End.
Engineer Zero 