> 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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