From: Axel Kohlmeyer (
Date: Mon Jan 31 2011 - 11:59:50 CST

On Mon, Jan 31, 2011 at 11:46 AM, B.M.B. Vanschouwen
<> wrote:
> Hello.


> I am trying to implement the script with VMD 1.8.6 on my PC, to
> generate a porcupine plot figure of the results, but I cannot figure
> out how to execute it.  Does anyone know how I would go about
> implementing this script?


this is more of a Tcl question than a VMD question.
so i suggest you have a look at some basic Tcl
tutorial to get an idea of what is going on, particularly
you want to learn something about how namespaces
work in Tcl.

the essense is listed in the header of the sources (but
not in sync with the code, so i suspect that namespace
feature was added later).

as it says there: source PorcupinePlot.tcl will load the
contents into VMD. however, if you are using the TkConsole
plugin, you should use "play PorcupinePlot.tcl" instead
(for technical reasons).

after that you can execute the embedded procedurec as






if you are lazy and don't want to type the namespace prefix
all the time, you can first do:

namespace porcupineplot import *

and then Diff, Traj, Remove, Help with the proper arguments.

how to use the individual embedded commands should be
explained at the location where you found the script or you
should better ask on the gromacs users mailing list, or contact
the author, if that fails.


> Bryan VanSchouwen

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.