<br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Stefan Hoorman wrote:<br>
> How can I calculate the angle between a helix inserted in a membrane and<br>
> the axis perpendicular to the surface of the membrane. I have tried<br>
> using g_helixorient, but the graphs all come as a straight line in zero.<br>
<br>
See -z in g_sgangle -h<br>
<br>
Mark<br>
<br>
<font color="#888888"><br></font></blockquote><div>Thank you for the tip, but again I faced a problem. I could only analyse using g_sgangle with an index group containing 3 atoms. Then the problem is, since my helix not only tilts, but also it bends a little back and forth, the angle between it and the z axis will vary greatly depending on which three atoms I choose. I imagined that by choosing three alpha carbon atoms every four residues would give me a good outcome, but it turns out that the angle changes a lot, and I am guessing it is because of this bending movement. When I say "changes a lot" I mean; it starts at 0º and gets up to 50º, which i imagine to be a little bit too much. <br>
Would there be a better way to calculate this?<br></div></div><br>