Ahh, after looking at my code for an hour straight (literally, my eyes stayed on the screen on my PowerBook without moving), I found my elusive bug. Guess what it was? Yep, I had used an '<=" instead of a '<' in my while loop all this code is in, causing my code to overshoot my 'protein_matrix' and throw undefined errors. This little bug has caused me like 3 days........grrrrrr You guys are great though. Thanks. I've learned a lot of valuable debugging routes from this thread... By the way: Does perl have exception handling?

**Special thanks to husker for introducing me to this online perl community**

In reply to Re^2: Understanding variable scope in perl by BioBoy
in thread Understanding variable scope in perl by BioBoy

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