[gmx-users] Re:Re: helix tilt

Stefan Hoorman stefhoor at gmail.com
Fri Dec 4 17:30:33 CET 2009

> 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?
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