an explanation on how you're seeing the dna

Maybe you are thinking that the DNA strands in the last few pictures doesn't really look like anything but beads on a chain? This is because the DNA strands used to build these cross motifs is being represented in PAM5. This is a convention that uses five groups to represent the major structural components of the DNA strand. I think, and correct me if I'm wrong, but there is a group (bead) to represent a phosphate, each of the two sugars, the nucleotides and the hydrogen bonding on the nucleotides. That's five. That's what I'm going with tonight. It is a hell of a lot easier to work with these groups than the atoms they represent. However I must admit the atomistic representation of the DNA chains is more visually appealing:

The octet sim is done in half the time I thought. It is no wonder I am usually early for appointments. I'll post it later tonight or tomorrow.

MTF