VMD-L Mailing List

From: Wei Gao (weigao05_at_gmail.com)
Date: Mon Jan 07 2013 - 17:20:48 CST

Never mind. I found the reference. $sel is Tcl proc created by VMD. Thanks!

Wei

On Mon, Jan 7, 2013 at 2:51 PM, Wei Gao <weigao05_at_gmail.com> wrote:

> 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****
>>
>> ** **
>>
>
>