[phenixbb] measuring the angle between two DNA duplexes

Pavel Afonine pafonine at lbl.gov
Mon Jan 20 09:47:11 PST 2014

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 
   - compute and report angle between those two lines?

Would this be helpful? Is it worth adding such tool?


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:lixiang1642 at gmail.com <mailto:lixiang1642 at gmail.com>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20140120/a123a70b/attachment-0001.htm>

More information about the phenixbb mailing list