From: Anthony Ivetac (
Date: Tue Nov 16 2004 - 08:53:35 CST


I am interested in calculating the angle formed between the axes of 2
domains in my protein, for different frames of a simulation trajectory.

I have used the script 'fit_angle.tcl' - see here:

This script takes 2 atom selections and fits a vector to each - it then
calculates the angle formed between the 2 vectors and outputs this. It
can do it for a single structure, and also multiple frames.

I am wondering how I can visualise the vectors it fits to the atoms in
VMD, superimposed onto my protein? Something like the
'cylinder-and-cone' representation used to draw principal axes in this

The orient.tcl script has a function to draw a vector, but I am not sure
which variables in the fit_angle.tcl script hold the vectors I need to
draw and how to do this.

Many thanks,