Ooh, pretty pictures

(Structural Biology)

Well, I just went out and bought a couple of textbooks. One of which styles itself as an introduction to proteomics (like genomics except for proteins). As such, the point where I have interesting things to post about in the Structural Biology dept is drawing closer.

There's one thing I need to cover first, though. Those pretty pictures of molecules that you see in textbooks? I need to be able to produce them. Fortunately there's an easy way to do this.

See, all these efforts to determine the shapes of various molecules can be summarised in a single file, generally a .pdb file (although there are many other formats). So you can go to, for example, Georgia State University's PDB page, download a few examples, and muck about with them using a suitable image viewer.

I haven't experimented much with the variety of viewers on offer, but the one I've been using so far seems good. It's called PyMOL (you can tell I'm a Python nut, can't you...). It's probably not as polished as a commercial viewer would be, but it's open source and pretty damn good at what it does. It also has lots of little extensions and scripting handles that I can't for the life of me figure out how to use. You can do movies with this thing.

Have a pretty picture.


The above picture is of a molecule of haemoglobin - I picked the PDB file pretty much at random from the GSU site mentioned above.

I currently have the book "Introduction to Protein Science" sitting on my desk next to me. This time, when I glanced at the cover, I thought "hmm... that molecule looks vaguely familiar". Then I took a closer look...

In the words of Nelson Munz: haha!


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