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.
Sincerely,
Xiang
2014/1/20 Pavel Afonine
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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-- Li Xiang Department of chemistry, Purdue University Email：[email protected]