BI/BII issue

[auffinger]

Hi Xiang-Jun,

BI-BII feature is nice. however, the criteria e-z is probably not sufficient to define one or the other since, the way you do it, every nucleotide is either of the BI or BII type. Furthermore, I think that BI/BII is mainly used for B-DNA.

Best,

Pascal

[xiangjun]

As noted in the -tor output file,

Code: [Select]

          e-z: epsilon - zeta
              BI:  e-z = [-160, +20]
              BII: e-z = [+20, +200]

The criteria are based on "Nucleic acid backbone parameters" at the Jena website. Do you have another definition?

Also, the BI/BII classification is purely backbone-based (epsilon and zeta torsion angles), not specific to "B-DNA" whose definition may require characterization of the base pair geometry.

Xiang-Jun

[auffinger]

OK, thanks for the link, I will look more into that and reply soon.

Pascal