Hi Xiang,

Since you mentioned "or in other software", I think I can chime in to this topic. The short answer is to see "How to calculate DNA bending angle?" (http://forum.x3dna.org/faqs/how-to-calculate-dna-bending-angle/).

3DNA, following the original NewHelix algorithm, calculates a best-fitted linear global helix (where sensible) using equivalent C1'...C1', RN9/YN1...RN9/YN1 atom pairs along each strand. The so-called global helical axis parameters are no longer widely used, but the best-fitted linear helical axis is a useful concept, and has been kept in 3DNA and DSSR [http://forum.x3dna.org/rna-structures/dssr-software-for-defining-the-(secondary)-structures-of-rna/].

HTH,

Xiang-Jun

--
Xiang-Jun Lu (PhD)
Email: xiangjun@x3dna.org
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/

>
> On 1/20/14, 5:48 AM, ?? wrote:
>
> Hi,
>
> I have a DNA model which is composed of two DNA duplexes. I want to
> measure the angle between the two duplexes and if there a way to do it in
> PHENIX or in other software?
>
> Thanks you very much for your help!
>
> Sincerely,
> Xiang
>
> --
> Li Xiang
> Department of chemistry,
> Purdue University
> Email?lixiang1642@gmail.com