Wednesday, August 29, 2007

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.


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