VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Apr 29 2014 - 09:16:43 CDT

On Tue, Apr 29, 2014 at 10:01 AM, Jean-Patrick Francoia
<jeanpatrick.francoia_at_gmail.com> wrote:
> Le 29/04/2014 15:54, Axel Kohlmeyer a écrit :
>
>> On Tue, Apr 29, 2014 at 8:49 AM, Jean-Patrick Francoia
>> <jeanpatrick.francoia_at_gmail.com> wrote:
>>>
>>> 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 ?
>>
>> find a program/tool that converts a SMILES string into a supported
>> file format and then load that file into VMD.
>>
>>> Regards
>>>
>>> JP
>>>
>>
>>
>
> I forgot to mention that:
>
> Yes I know a bunch of softwares like Avogadro to visualize/export a SMILES
> string, but most of them can't handle my number of amino acids (>15000).
> That's another specification. I know VMD is pretty fast compared to Avogadra
> for example, when it comes to open a file.

but you *do* need a SMILES interpreter. VMD only reads coordinates. 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.