Stefan Hoorman wrote:
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
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?
I don't know, I've never seen them. I'd be expecting three numbers in
each to indicate a vector parallel to the axis.
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.
This is standard geometry - dot-products of vectors are related to the
cosine of the angle between them. Check wikipedia.
Mark
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