[phenixbb] measuring the angle between two DNA duplexes

[jens j birktoft]

Pavel,

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

Cheers

Jens


-- 
+++++++++++++++++++++++++++++++++++++++++++++++++++
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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