I came across across a bug in the RALEE code that processes the secondary structure line in Stockholm files. The Stockholm file (of vault proteins) just happened to break the code that processes how many helices there are and associates a helix number with each base pair position. Here are the cases that I had to fix:
If there isn't another separate helix within the sequence, the helices that aren't separated by unpaired nucleotides can't be detected in the original code. I was able to fix the bug by adding more cases. Hopefully I haven't created another bug.