Week 2

This week was reserved for testing the program to make sure that the method I included (only) does what it supposed to do.

It (only) supposed to count the native connections, between amino acids, in which tryptophan is involved within a given protein conformation for all conformations of a road map.

So, I looked at the amino acid sequences of proteins, run the program, counted native connections between amino acids by hand, and compared this with the results of the program. I did this for some number of conformations and different amino acid sequences.

I figured out that it indeed does count right for any given conformation, but then there was a problem. So, I started digging through the code. It took me a while to find where exactly the mistake was, but then, thanks go to my Graduate Student Mentors, the problem could quickly be solved.

At the end of the week the program was running smoothly. I did print the first test plots for a small complete road map. It was exciting. The results matched with what I thought, which is great. However, there is still a long way to go. Other than that, I set up my web page. I wish the web page would run as good as the program already.