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General discussions (Q&As) / defining a local helix axis

« on: July 08, 2009, 01:23:01 pm »

I am analyzing a protein-DNA complex in which the DNA is somewhat underwound and may have several small kinks. I wanted to calculate the helical trajectory along the DNA helix and wondered if I could use 3DNA to do this. 3DNA output gives coordinates for the origin of each base pair (Ox,Oy,Oz) as well as coordinates for the position (Px,Py,Pz) for each dinucleotide step. Would one or the other of these coordinate sets be more appropriate to use, or are neither of these a good measure of the helix axis?

Thanks!