From: Francesco Pietra (
Date: Sun Mar 07 2010 - 02:55:03 CST

New to trajectory_path.tcl, I dare placing a question. In my usage

source trajectory_path.tcl
set myligand [atomselect top "resid for.myligand"]
trajectory_path $myligand scale (which, grossly scales from red to
yellow, cyan and finally blue)

there is a large shift in the coordinate scale between the path that
can be followed from VMD Main and that described with
trajectory_path.tcl. Also, although the two are identical, the latter
is on a much smaller scale. The shift is so large that the path
described with trajectory_path.tcl is seen entirely at the immediate
outside of the protein.

francesco pietra