VMD-L Mailing List

From: Nitin Bhardwaj (nbhard2_at_uic.edu)
Date: Tue Mar 29 2005 - 13:18:20 CST

Hi,
  I have a protein that is known to bind to membrane. Now all that is
known are some key residues that interact with the membrane. Now, I need
to know the orientation (in term of euler angles) of the normal to the
plane (representing the membrane which I will form by drawing the plane
through any of the three interacting residues) with respect to the Z-axis.

Here is what I will do:

Calculate the equation of the plane passing through any of the three
residues ineracting with the membrane. Form a plane using the "Graphics"
command in VMD.

Here is what I need to know:
 What is the relative orientation of the normal of this plane with respect
to the Z-axis. In other words, what total rotation (around any or all
three axes) would make the normal to the plane make it coincide with the
Z-axis.

Is there a way I can find the angles that the protein needs to rotate so
that the normal coincides with the Z-axis (apart from trial and error).

Also is there a better way to do this entire thing including the first
part (knowing the equation and formation of the plane). I somehow do not
feel like picking up my pen and calculating the equation.

Thanks,
Nitin