Thursday, September 24, 2009

Sitting at my terminal...

So I'm in my first rotation, and it's going pretty darn well so far. However, I made a grave miscalculation on Monday, and am still paying for it. I'm working on molecular modeling, where I use computers to help characterize and test potential protein structures. It's pretty awesome, I think. My project is to try and determine the closed state of a particular membrane protein. We know (well, we're pretty sure) what the open state looks like, but no one has been able to determine the closed state. X-ray diffraction and crystallography aren't helping either at the moment, because the darn thing doesn't want to crystallize in the closed state-only the open. And it's got to shut off some time... Anyway, I've been working on a scripting code (I feel so nerdy!) that lets me take a part of the protein, move it through space, and see if that's a possible structure. If it's possible (based on Van der Waals interactions and sterics), then my program calculates the energy of each and every atom, so I can determine the gating charge. We know what the value should be. So, it's pretty much guess and check. I guess a structure, check the value, and either keep or punt it. So far, I've been doing a lot of punting.

Monday, I got the best version of my program ready, set it to run 20808 structures, and pushed 'go'. I thought it would take eleven hours (finishing before dawn Tuesday). It's been almost three days... It's still thinking. I keep going over the code, because I'm convinced there's a glitch. But I won't know until around 4 today, which, unfortunately, is when the University is going on lock down. There's some silly convention thingy that's taking over here. I think they call it the G20?

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