VMD-L Mailing List
From: Jean-Patrick Francoia (jeanpatrick.francoia_at_gmail.com)
Date: Tue Apr 29 2014 - 15:51:45 CDT
Le 29/04/2014 21:11, Eduard Schreiner a écrit :
> Hi all,
> I would also like to mention the free tool EMC
> which I use a lot to build any type of amorphous system or polymer
> without a specific secondary structure, all based on SMILES definition
> of all the components.
> On Tue, Apr 29, 2014 at 6:56 PM, Davide Provasi
> <davide.provasi_at_gmail.com <mailto:davide.provasi_at_gmail.com>> wrote:
> Chemaxon has tools and Java libraries to convert smiles to formats
> vmd can visualize
> 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.
> 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
> On Tue, Apr 29, 2014 at 11:01 AM, Norman Geist
> <mailto: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
> 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 <mailto: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 <tel:212-659-8618>
> Fax: 212-849-2456 <tel:212-849-2456>
EMC seems to be exactly what I need. How many atoms do you have to
handle by SMILES string ? It seems to be a lot, from what I saw on some
Would you have any usefull links to start ? The doc provided in the
package is just documentation.