Thanks XAvier and George for the reply. Yes the N and C terminus are on the opposite sides of the bilayer. So I can take the values of the even TMs as (180 - respective value), correct?<br><br>Regards,<br><br>Anirban<br><div style="visibility: hidden; display: inline;" id="avg_ls_inline_popup">
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<div class="gmail_quote">On Fri, Jun 4, 2010 at 8:00 PM, George Khelashvili <span dir="ltr"><<a href="mailto:gek2009@med.cornell.edu">gek2009@med.cornell.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
Your 150 degree angle is in reality 30 degrees (180-30). This is a matter of defining the vector representing your helix vs. the direction of the z axis. If your vector points in the opposite direction of the z axis, then your angle will be between 90 and 180 degrees.<br>
<br>
George<div><div></div><div class="h5"><br>
<br>
Anirban Ghosh wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi ALL,<br>
<br>
I am using g_angle to calculate the tilt of individual helix in a rhodopsin GPCR with respect to z axis. In the index file I am defining the top and bottom of each helix with first 4 and last 4 residues of that helix respectively. Strangely, I am getting the tilt angle of the odd helices like TM1, 3 and 5 in the range of 30 degrees, but the even helices TM2, 4 and 6 are giving value in the range of 150 degrees. But visual inspection of the simulation does not show such huge deviation. Why is it giving so? Am I doing anything wrong here? Any suggestion is welcome. Thanks a lot in advance.<br>
<br>
Regards,<br>
<br>
Anirban<br>
</blockquote>
<br>
<br></div></div>
-- <br><font color="#888888">
George Khelashvili, Ph.D.<br>
Department of Physiology and Biophysics<br>
Weill Medical College of Cornell University<br>
1300 York Avenue, Room LC501<br>
New York, NY, 10065, USA<br>
<a href="mailto:gek2009@med.cornell.edu" target="_blank">gek2009@med.cornell.edu</a><br>
Phone: 1-212-746-6539<br>
Fax: 1-212-746-6226</font><div><div></div><div class="h5"><br>
<br>
<br>
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