Stefan Hoorman wrote:
Stefan Hoorman wrote:
> How can I calculate the angle between a helix inserted in a
membrane and
> the axis perpendicular to the surface of the membrane. I have tried
> using g_helixorient, but the graphs all come as a straight line
in zero.
See -z in g_sgangle -h
Mark
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.
Would there be a better way to calculate this?
g_principal will calculate the axes of inertia, from which you can
calculate the angle with the Z-axis.
Mark
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