From: Wei Gao (weigao05_at_gmail.com)
Date: Mon Jan 07 2013 - 14:51:11 CST

Dear Peter,

Thanks for your help! The script is really helpful.
I understand most of it, but since I am still a baby in Tcl scripting, not
clear about the following commands:

$sel frame $iFrame
$sel set user $data
$sel delete

where can I find reference for the above commands that are started with
variables? Are "frame" and "delete" commands?

Thanks,
Wei

On Mon, Jan 7, 2013 at 2:56 AM, <peter.schmidtke_at_fr.netgrs.com> wrote:

> Dear Wei,****
>
> ** **
>
> You can add user defined values to each atom in a similar way as b-factors
> or occupancies. Then you can colour for instance your atoms by this value
> (trajectory -> user …) In order to read and assign such user defined values
> per atom you have to do a little scripting. I attached a sample script that
> reads in txt files containing on each line one value for an atom and
> assigns this value to the atom “$sel set user $data”.****
>
> ** **
>
> Read a bit the documentation of vmd and tcl scripting, normally there is
> enough on the web on these things.****
>
> ** **
>
> Best regards.****
>
> ** **
>
> Peter Schmidtke****
>
> ** **
>
> ** **
>
> --****
>
> Post-Doc (Molecular Modeling)****
>
> CPMM****
>
> Institut de Recherches Servier****
>
> Croissy-sur-Seine (France)****
>
> ** **
>
> ** **
>
> ** **
>
> *De :* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *De la
> part de* Wei Gao
> *Envoyé :* samedi 5 janvier 2013 17:43
> *À :* vmd-l_at_ks.uiuc.edu
> *Objet :* vmd-l: how to plot per-atom field variable****
>
> ** **
>
> Dear All,
>
> ****
>
> Does anyone know how to plot per-atom variable such as stress/atom in VMD?
> Just like the way that VDM plotting position in "Coloring method->position".
> ****
>
> Thanks,****
>
> Wei****
>
> ** **
>