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Hi Xiang,<br>
<br>
phenix.angle computes angle between two lines. Lines can be define
two ways:<br>
<br>
- by two pairs of points with each pair defining two points that
line passes through:<br>
<br>
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)"<br>
<br>
here atom selection<br>
"chain A and (resseq 1 and name CA or resseq 2 and name CA)"<br>
defines two points, and atom selection<br>
"chain B and (resseq 1 and name CA or resseq 2 and name CA)"<br>
defines another two points.<br>
<br>
- 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:<br>
<br>
phenix.angle model.pdb "chain A" "chain B"<br>
<br>
here "chain A" defines first helix, and "chain B" defines second
helix.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/16/14 6:58 AM, 李翔 wrote:<br>
</div>
<blockquote
cite="mid:CAE5L1v8MFEF_3SRgDkLhLCH3sG-jbepSaVj6aYAmRPz=YDPDCA@mail.gmail.com"
type="cite">
<div dir="ltr">Hi,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Thanks for your help!</div>
<div><br>
</div>
<div>Sincerely,</div>
<div>Xiang<br>
-- <br>
<div class="gmail_signature">Li Xiang <br>
Department of chemistry,<br>
Purdue University<br>
Email:<a moz-do-not-send="true"
href="mailto:lixiang1642@gmail.com">lixiang1642@gmail.com</a></div>
</div>
</div>
<br>
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<br>
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