[phenixbb] how to use phenix.angle command?
pafonine at lbl.gov
Tue Dec 16 07:32:09 PST 2014
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
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.
On 12/16/14 6:58 AM, 李翔 wrote:
> 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
> Thanks for your help!
> 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
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