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! Sincerely, Xiang ----- Original Message ----- From: "Xiang-Jun Lu" <[email protected]> To: [email protected] 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-(second... ]. HTH, Xiang-Jun -- Xiang-Jun Lu (PhD) Email: [email protected] 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? [email protected]

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb