Ed's Big Plans

Computing for Science and Awesome

Archive for the ‘Featured’ Category

Squishy TIM Barrel Subunits

without comments

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).

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…

1a5m_1_3 1a5m_2_3 1a5m_3_3

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

Eddie Ma

October 14th, 2009 at 9:49 am

New Diagram for MSc-X3 (math paper)

without comments

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.

Some Assembly Required.

Eddie Ma

August 20th, 2009 at 12:08 pm

Zinc, the Entertainment Unit

with 3 comments

Firefox Eats Cara's TV

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 RFA

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 😀

Eddie Ma

July 12th, 2009 at 4:25 pm

Monet Molecules c/o Autotrace

with one comment

A Monet Isopentenol c/o Autotrace

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.

Eddie Ma

July 9th, 2009 at 2:56 pm

Posted in Featured,Technology