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Welcome => Feature requests => Topic started by: auffinger on August 04, 2012, 02:34:45 pm

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Title: BI/BII issue
Post by: auffinger on August 04, 2012, 02:34:45 pm
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
Title: Re: BI/BII issue
Post by: xiangjun on August 04, 2012, 03:13:30 pm
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 (http://www.imb-jena.de/Piet/help/backbone.html)" 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
Title: Re: BI/BII issue
Post by: auffinger on August 05, 2012, 01:13:02 pm
OK, thanks for the link, I will look more into that and reply soon.

Pascal

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.