From: Bennion, Brian (
Date: Tue Mar 07 2017 - 12:07:27 CST


The tcl code for this package is easily modified. I wanted to know the angle between system z-axis and the molecules principle axis. I just stuck an extra variable to catch the angle after it was calculated and spit it out at the end of the analysis.


From: [] On Behalf Of sunyeping
Sent: Monday, March 06, 2017 19:32
To: vmd-l <>
Subject: vmd-l: Usage of the Orient package

Dear all,

By using Orient package I can draw the three prinicipal axes and rotate the molecule to align it to the x, y, z direction. And we can also get the variable I, the inertia tensor. However, how could I get the information of the principal axes? For example, I have a MD trajectory of a protein and I wish to get the coordinates of a principal axis ( represented by the x, y, z coodinates of two points: the mass center and another point in the principal axis) of the protein in each frame, then how should I calculate for that?

Best regards,

Yeping Sun