[phenixbb] how to use phenix.angle command?

[Pavel Afonine]

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：lixiang1642 at gmail.com <mailto:lixiang1642 at gmail.com>
>
>
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> phenixbb mailing list
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