[phenixbb] measuring the angle between two DNA duplexes

Xiang Li li338 at purdue.edu
Sun Jan 26 08:05:19 PST 2014

Hi Xiang-Jun,

Thanks for your previous email with the suggestions! I met a problem here that my computer with Linux system is down and is there anyway 3dna can run on a window system? 

Btw, I want to generate a 42 mer DNA duplex with 10.5 bp per turn, can 3dna do that?

Thanks a lot for your kind help!


----- Original Message -----
From: "Xiang-Jun Lu" <3dna.lu at gmail.com>
To: phenixbb at phenix-online.org
Sent: Tuesday, January 21, 2014 11:58:28 AM
Subject: Re: [phenixbb] measuring the angle between two DNA duplexes

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/ ]. 



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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