Yes,
or inverse your sections from the index!
On Jun 5, 2010, at 10:10 AM, Anirban Ghosh wrote:
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?
Regards,
Anirban
On Fri, Jun 4, 2010 at 8:00 PM, George Khelashvili <gek2...@med.cornell.edu
> wrote:
Hi,
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.
George
Anirban Ghosh wrote:
Hi ALL,
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.
Regards,
Anirban
--
George Khelashvili, Ph.D.
Department of Physiology and Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Room LC501
New York, NY, 10065, USA
gek2...@med.cornell.edu
Phone: 1-212-746-6539
Fax: 1-212-746-6226
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