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
> 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:
>>> I wonder if there is a way to visualize a SMILES string in VMD, and
>>> 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.
> 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.