[phenixbb] measuring the angle between two DNA duplexes
li338 at purdue.edu
Sun Jan 26 08:05:19 PST 2014
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
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
> On 1/20/14, 5:48 AM, ?? wrote:
> 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!
> Li Xiang
> Department of chemistry,
> Purdue University
> Email? lixiang1642 at gmail.com
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