VMD-L Mailing List

From: Davide Provasi (davide.provasi_at_gmail.com)
Date: Tue Apr 29 2014 - 11:56:16 CDT

Chemaxon has tools and Java libraries to convert smiles to formats vmd can
visualize
(e.g. https://www.chemaxon.com/marvin/help/applications/molconvert.html)
It requires a license but it's free for non-commercial use.
the Corina web demo is also free and would generate high quality 3D
molecular structures.
http://www.molecular-networks.com/online_demos/corina_demo
these tools, however are optimized for small molecules;
I'm not sure how well they would perform on peptides, let alone long
proteins
good luck

Davide

On Tue, Apr 29, 2014 at 11:01 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> 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
> visualization-, than a building-tool, although it can be used for
> parameterization.
>
> Norman Geist.
>
> > -----Ursprüngliche Nachricht-----
> > Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> > Auftrag von Jean-Patrick Francoia
> > Gesendet: Dienstag, 29. April 2014 14:49
> > An: vmd-l_at_ks.uiuc.edu
> > 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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-- 
Davide Provasi
Dept. of Structural and Chemical Biology
Mount Sinai School of Medicine
Icahn Medical Institute Building
1425 Madison Avenue, Box 1677
New York, NY 10029-6574
Tel.:212-659-8618
Fax: 212-849-2456