From: Axel Kohlmeyer (
Date: Tue Apr 29 2014 - 10:50:28 CDT

On Tue, Apr 29, 2014 at 11:01 AM, Norman Geist
<> wrote:
> I don't think this is possible even with scripting, as "building" tools do
> usually have a database with coordinate templates. How could you otherwise
> determine the position of the atoms while adding them? VMD is more a

well, for amino acid sequences it *is* possible. only you have to
provide information about the secondary structure. in fact, there is
such a tool included in the molefacture plugin within VMD (Molefacture
Protein Builder). If that works, it most certainly should be possible
to script building any amino acid sequence. again, the issue is that
you have to make a choice for the secondary structure information.

> visualization-, than a building-tool, although it can be used for
> parameterization.

and a lot of other things. however, most of the add-on features work
by interfacing to some other software and placing that feature into a
Tcl extension plugin etc.

> Norman Geist.
>> -----Urspr√ľngliche Nachricht-----
>> Von: [] Im
>> Auftrag von Jean-Patrick Francoia
>> Gesendet: Dienstag, 29. April 2014 14:49
>> An:
>> Betreff: vmd-l: Visualize a SMILES string
>> Hello,
>> I wonder if there is a way to visualize a SMILES string in VMD, and
>> possibly in 3D. I did a bit of digging but found nothing clear.
>> How do you do that ?
>> Regards
>> JP
> ---
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Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.