From: Anthony Ivetac (ivetac_at_biop.ox.ac.uk)
Date: Tue Nov 16 2004 - 08:53:35 CST

Hi,

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:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-2279/fit_angle.tcl

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
script:

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/orient/

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,

Tony