<div dir="ltr">Hi Pavel,<div><br></div><div>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.</div>
<div><br></div><div>Sincerely,</div><div>Xiang</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014/1/20 Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov" target="_blank">pafonine@lbl.gov</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Xiang,<br>
<br>
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.<br>
<br>
phenix.angle model.pdb selection="chain A and resseq 1:123"
selection="chain B and resseq 20:345"<br>
<br>
The underlying procedure would do the following:<br>
- extract two sets of coordinates of atoms corresponding to two
provided atom selections;<br>
- draw two optimal lines (LS fit) passing through the above sets
of coordinates;<br>
- compute and report angle between those two lines?<br>
<br>
Would this be helpful? Is it worth adding such tool?<span class="HOEnZb"><font color="#888888"><br>
<br>
Pavel</font></span><div><div class="h5"><br>
<br>
<div>On 1/20/14, 5:48 AM, ���� wrote:<br>
</div>
</div></div><blockquote type="cite"><div><div class="h5">
<div dir="ltr">Hi,
<div><br>
</div>
<div>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?</div>
<div><br>
</div>
<div>Thanks you very much for your help!</div>
<div><br>
</div>
<div>Sincerely,</div>
<div>Xiang<br clear="all">
<div><br>
</div>
-- <br>
Li Xiang <br>
Department of chemistry,<br>
Purdue University<br>
Email��<a href="mailto:lixiang1642@gmail.com" target="_blank">lixiang1642@gmail.com</a>
</div>
</div>
<br>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Li Xiang <br>Department of chemistry,<br>Purdue University<br>Email��<a href="mailto:lixiang1642@gmail.com">lixiang1642@gmail.com</a>
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