VMD-L Mailing List

From: Jean-Patrick Francoia (jeanpatrick.francoia_at_gmail.com)
Date: Wed Apr 30 2014 - 01:37:00 CDT

Le 30/04/2014 08:23, Eduard Schreiner a écrit :
> there are examples coming with it. Still, I do not think it is a good
> idea to build a protein with 15000 amino acids with emc. You will get
> some amorphous mass.
>
> eddi
>
>
> On Tue, Apr 29, 2014 at 10:51 PM, Jean-Patrick Francoia
> <jeanpatrick.francoia_at_gmail.com
> <mailto:jeanpatrick.francoia_at_gmail.com>> wrote:
>
> Le 29/04/2014 21:11, Eduard Schreiner a écrit :
>> Hi all,
>>
>> I would also like to mention the free tool EMC
>>
>> http://montecarlo.sourceforge.net/emc/Welcome.html
>>
>> 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.
>>
>>
>> eddi
>>
>>
>>
>>
>>
>> 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
>> (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
>> <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
>> parameterization.
>>
>> Norman Geist.
>>
>> > -----Ursprüngliche Nachricht-----
>> > Von: owner-vmd-l_at_ks.uiuc.edu
>> <mailto:owner-vmd-l_at_ks.uiuc.edu>
>> [mailto: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 websites.
>
> Would you have any usefull links to start ? The doc provided in
> the package is just documentation.
>
> Thanks
>
>

No, there is "only" 960 amino acids :) So, how would you translate a
SMILES chain that long into an exploitable PDB ?

Regards