<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;">
<br>
Stefan Hoorman wrote:<br>
><br>
> Stefan Hoorman wrote:<br>
> > How can I calculate the angle between a helix inserted in a<br>
> 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<br>
> in zero.<br>
><br>
> See -z in g_sgangle -h<br>
><br>
> Mark<br>
><br>
><br>
> Thank you for the tip, but again I faced a problem. I could only analyse<br>
> using g_sgangle with an index group containing 3 atoms. Then the problem<br>
> is, since my helix not only tilts, but also it bends a little back and<br>
> forth, the angle between it and the z axis will vary greatly depending<br>
> on which three atoms I choose. I imagined that by choosing three alpha<br>
> carbon atoms every four residues would give me a good outcome, but it<br>
> turns out that the angle changes a lot, and I am guessing it is because<br>
> of this bending movement. When I say "changes a lot" I mean; it starts<br>
> 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>
<br>
g_principal will calculate the axes of inertia, from which you can<br>
calculate the angle with the Z-axis.<br>
<br>
Mark<br>
<br></blockquote></div>Ok, thank you for the info, but now I got a little bit confused. What exactly does the info from axis1.dat, axis2.dat, axis3.dat and moi.dat mean? And how would I use this info to calculate the helix tilt. I know the general meaning of principal axes of inertia, but I could not find any information more specific to this type of caltulation I need to do. If you could give any reference or any other type of information a little bit more specific I would be very greatful. I mean, if it is not too much to ask.<br>
Thank you<br>Stef.<br>