[phenixbb] measuring the angle between two DNA duplexes

Xiang Li li338 at purdue.edu
Mon Jan 20 10:41:54 PST 2014

Hi Jens,

Nice to see you in the email list here! I did no know hat before that you are in the list.:) 

I think there is a way to measure the angles between alpha helixes for protein in pymol which should be somehow the similar for DNA. I am trying to wrap up the rest of the data so I asked a few questions here.


----- Original Message -----
From: jens j birktoft <birktoft at nyu.edu>
To: PHENIX user mailing list <phenixbb at phenix-online.org>
Sent: Mon, 20 Jan 2014 13:12:38 -0500 (EST)
Subject: Re: [phenixbb] measuring the angle between two DNA duplexes
For us DNA people (we clearly are a minority) I think this would be a very
useful addition. Either a script or as part of the GUI would be OK
Jens J. Birktoft
Director of Crystallography
Structural DNA Nanotechnology
New York University
e-mail: jens.knold at gmail.com; Phone: 212-749-5057
very slow-mail: 350 Central Park West, Suite 9F, New York, NY 10025
On Mon, Jan 20, 2014 at 12:47 PM, Pavel Afonine <pafonine at lbl.gov> wrote:
> Hi Xiang,
> there is no ready-to-use tool for this right now, but I can spend a few
> moments and add one so it's available in next Phenix nightly build in a day
> or two.
> phenix.angle model.pdb selection="chain A and resseq 1:123"
> selection="chain B and resseq 20:345"
> The underlying procedure would do the following:
> - extract two sets of coordinates of atoms corresponding to two provided
> atom selections;
> - draw two optimal lines (LS fit) passing through the above sets of
> coordinates;
> - compute and report angle between those two lines?
> Would this be helpful? Is it worth adding such tool?
> Pavel
> On 1/20/14, 5:48 AM, 李翔 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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