VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Tue Apr 29 2014 - 09:57:05 CDT

JP,

SMILES only encodes molecular graph information and does not contain any 3-dimentional coordinate information. It is largely used for storing 2D small molecule structures in databases as 1D text strings. I don't know your use-case, but I would guess that you are better off using a different format.

Regards,
Christopher Mayne

On Apr 29, 2014, at 9:01 AM, Jean-Patrick Francoia 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.
>