Two of them are discussed in some detail below. The first is a DNA Duplex Generator that was the very first nab generated module. The second is a DNA Bender that shows the power of this approach. DNA Duplex Generator. The inputs are the sequence of one strand and four numbers that define the duplex's X-offset, inclination, twist and rise.
Duplex creation requires two steps.
The name of the module it generates is dna . The parameter seq has no default. The traditional way of doing this is to select and interactively change the relevant torsion angles. Unfortunately, due the complexity of the DNA backbone, several torsion angles may need to be changed in a concerted fashion to achieve the desired base positions. And to make things even worse, these torsion angle movements will not move the complementary strand which is only hydrogen bonded to the strand being bent.