[phenixbb] measuring the angle between two DNA duplexes

[Xiang-Jun Lu]

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 at 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 at gmail.com
>
>
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