Jack

It's been a fairly boring and uneventful week; mostly I've been doing preparatory work. I downloaded VMD (a visualization program) onto the computer that I use, and spent a day and a bit figuring out how to work it. Most of the basic functions were pretty simple (changing the display options, measuring distance between atoms) but some of the analytically tools took longer to learn (free energy calculators, RMSD trajectories, etc.). Reading through the NAMD tutorial (NAMD is the program we use for actually simulating molecules) was death, as the prose was incredibly dense and boring. I also spent a little time familiarizing myself with the bibliographical tools used by the group, and made a mock entry to test it out.
I also had a meeting with Dr. York, where we discussed what primary research to read, what background to read up on, and more like that. I did finally get a concrete project, though-I'm going to be using novel methods to attempt to determine what causes the minimal sequence Hammerhead Ribozyme to switch from its catalytically in-active to its catalytically active state.
Since my last post, I had a chance to meet some of the other researchers in the group, including the three PhD candidates that moved here with Dr. York from Minnesota. They're very friendly and have taken me in, as it were, and even invited me rock climbing, which is a sort of group activity for the lab. I also got to go to a picnic for a recent PhD recipient and meet some of the people from the other labs in the building. All in all, a productive week.