Ed's Big Plans

Again with the TIM Barrel pictures! Here’s some text about it from my notes…

1a5m (A Urease) is a really interesting protein– it consists of three subunits. Each subunit consists of three unique domains: a very squashed TIM Barrel, an alpha-alpha-alpha-beta-beta domain and a beta-beta-alpha-beta-beta domain. I’m not yet sure what to call little broken alpha helices that have less than two complete turns. The TIM Barrel (though exceedingly asymmetrical) will still be accounted for in the data to be analyzed. The TIM Barrel (566 amino acids) is the alpha subunit of each symmetrical subunit. The remaining two domains are the alpha and beta subunit though PDB is not clear which is which: they each weigh in at 100 and 101 amino acids. 1a5m is part of several solved urease structures in the PDB– the collection: {1A5K, 1A5L, 1A5M, 1A5N, 1A5O} are solved by Pearson et al. (1998).

References
Matthew A. Pearson, Ruth A. Schaller, Linda Overbye Michel, P. Andrew Karplus, and, Robert P. Hausinger (1998). Chemical Rescue of Klebsiella aerogenes Urease Variants Lacking the Carbamylated-Lysine Nickel Ligand. Biochemistry. 37(17):6214-20.

Squishy squishy shapes– the giant pink object in the next picture is actually three such TIM Barrels, each of which belongs to one of the three subunits.

Each of the three subunits are shown separately below…

Aesthetically pleasing– these images were captured from the JMol output available from RCSB PDB.

Brief: I’m particularly happy with this diagram… I had something along these lines in my head for a while, but I never could figure out how to draw it correctly. I never thought that simplifying it to three easy steps was the smarter thing to do.

A Most Disturbing Story
(…on Youtube)

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… Later that week, I brought the remnants of wedding cake to iGEM, but that’s a story for another day …

Mmm mmm…

Firefox Eats Cara's TV

Way back at the beginning of this month, I sent away to Apple to order a DVI-I to S-Video / RCA connector. The total cost was $35 after shipping and tax, so it was well worth it as now I’ve gotten yet more value out of the Mac Mini.

The circa 1980′s television set can now play all of the media that is on the network, on the internet or on whatever other storage you can plug into Zinc, the Mac Mini.

DVI-I to S-Video and RCA

Technical Stuff about DVI Connectors

When looking for a DVI to RCA video connector, the wrong thing to do is to go to a big computer shop. These places will turn you away and tell you the part doesn’t exist. Heck, even the hobby shops failed to provide it or give any useful information. And you know– they’re half right. There’s no such thing as a DVI-D to RCA connector, because the former is a digital signal, and the latter is an analogue signal. The DVI-I is port is offers a combined digital and analogue signal, that’s how it can be converted out to such a large variety of display devices. It’s one of the selling points that Apple discusses about its laptops and other machines.

Buy it or not…

If you purchased a computer with a DVI-D output, you won’t be able to use Apple’s connector– so don’t try, you’ll waste your money and be frustrated– however, if you have a machine with DVI-I output, then this thing will work for you too even though big and small shops alike will tell you the connector doesn’t exist.

Simply Charming

I also got two charming flotation device / pillow / toys packaged with the connector!

Conclusion: I’m happy

A Monet Isopentenol c/o Autotrace

Brief: Happy accidents make me happy– here’s isopentenol after grabbing it as an SDF out of PubChem, dumping it out into a PNG with Bioclipse, grayscaling it with GIMP– then converting it to an SVG with Autotrace (RO IT Systems)… It’s just pretty… like a Monet. Of course, I have to go back and make it look like a molecule again for a paper… but I’m going to admire the pretty little alcohol for a bit.

Zinc grows an eyeball.

So, before Cara and I left home yesterday, I decided on a whim to quickly attach an ancient webcam to Zinc to use as an ad hoc surveillance device — well ok, it’s mostly for fun. This webcam was actually purchased and used with Bronze (my very first laptop), so the refresh rate, white balance and optical zoom are all from circa 2004.

Here, Zinc’s eyeball has been mounted with macam and works like a charm. The frame rate is inexcusably horrendous– but over a VNC connection, I seriously don’t care.

Eventually, Zinc will use macam’s quicktime application component to automatically shoot a photo once every x minutes, and send an e-mail to me if there is significant optical difference between the two images. In a stagnant room– this is not very challenging technically.

Giving Zinc an eyeball has granted us more peace of mind whenever we decide to travel– thus improving again the value of the mac mini… wait till you see what I’ve got planned next…