Re: [phenixbb] measuring the angle between two DNA duplexes

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. Sincerely, Xiang ----- Original Message ----- From: jens j birktoft To: PHENIX user mailing list Sent: Mon, 20 Jan 2014 13:12:38 -0500 (EST) Subject: Re: [phenixbb] measuring the angle between two DNA duplexes 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: [email protected]; 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 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：[email protected]

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