[phenixbb] measuring the angle between two DNA duplexes

李翔 lixiang1642 at gmail.com
Mon Jan 20 10:57:39 PST 2014

Hi Pavel,

Thanks a lot for the reply! I think it will be helpful for the guys work
with DNA like me. If I remember right, in Pymol there is a way to measure
the angles for alpha helices and it should very similar to calculate the
angles for DNA duplexes. But there is not a way to do it. It will great if
PHENIX can do the measurement like this.


2014/1/20 Pavel Afonine <pafonine at lbl.gov>

>  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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Li Xiang
Department of chemistry,
Purdue University
Email:lixiang1642 at gmail.com
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