Hi Xiang,

phenix.angle computes angle between two lines. Lines can be define two ways:

- by two pairs of points with each pair defining two points that line passes through:

phenix.angle model.pdb "chain A and (resseq 1 and name CA or resseq 2 and name CA)" "chain B and (resseq 1 and name CA or resseq 2 and name CA)"

here atom selection
"chain A and (resseq 1 and name CA or resseq 2 and name CA)"
defines two points, and atom selection
"chain B and (resseq 1 and name CA or resseq 2 and name CA)"
defines another two points.

- or alternatively you specify two sets of points (for example two helices) and the program will output the angle between the longest principal axes. Example:

phenix.angle model.pdb "chain A" "chain B"

here "chain A" defines first helix, and "chain B" defines second helix.

Pavel

On 12/16/14 6:58 AM, 李翔 wrote:

Hi,

I am trying to measure the angle between two DNA duplex domains. I used phenix.angle command for calculation. However, I get a wrong answer. Can anyone talk a little bit more details on this command please? I used a single strand DNA from each duplex to calculate the angle which I thought it might be working since it is calculating the axis.

Thanks for your help!

Sincerely,

Xiang
--

Li Xiang
Department of chemistry,
Purdue University
Email：[email protected]
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