VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Feb 18 2013 - 08:57:09 CST

On Mon, Feb 18, 2013 at 2:26 PM, Davide Mercadante
<dmer018_at_aucklanduni.ac.nz> wrote:
> Dear All,
>
> Please accept my apologies if I am rising a stupid issue. I am trying to run
> the spring.tcl script available in the VMD-script library without any
> success so far and I am not able to understand what I am doing wrong.
> I successfully source the script with the command source script.tcl (the
> script is placed in the same DIR of the pdb file).
>
> Then I perform an atom selection for the atom where I want the spring to be
> drawn using the following command:
>
> atomselect 0 "index 5"
>
> And I get as a result of that an atom selection called atomselect0.
>
> Then I try to recall the proc spring that is in the spring.tcl file (the
> procedure doesn't seem to have any argument – spring {} ). However, I get
> the following error:
>
> can't read "vmd_pick_mol": no such variable
>
> I think I am specifying the atomselection but somehow I am missing the
> molecule selection? In the atomselect command the "0" is to define molid 0,
> so why the script doesn't pick up the vmdpickmol variable?
> Apart from the atomselect command do I need to issue any additional command
> before calling the script?

there are two problems.

1) you are misunderstanding the instructions. the atomselect command
has no effect and is not what the instructions call for.
2) the script was written a very long time ago for a rather different
version of VMD. the handling of "pick" events has since changed.

thus you'll have to modify the script

you can replace $vmd_pick_mol with top
and $vmd_pick_atom with your desired atom index.

a more elegant solution would be to pass the information as arguments
to the script.

axel.

>
> Thank you very much for your help.
>
> Cheers,
> Davide
>
> **********************************************
> Davide Mercadante Ph.D.
> Postdoctoral Fellow
> Heidelberg Institute for Theoretical Studies – HITS
> Schloss-Wolfsbrunnenweg, 35
> D-69118 Heidelberg, Germany.
> **********************************************
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.