[Chimera-users] Using Chimera to read SMILES string into structure

[Elaine Meng]

Hi George,
The smiles->3D conversion is done by a Web service at Indiana  
University, and as far as I know it uses the standard SMILES notation  
as described by Daylight:
http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html

However, I did reproduce the problem you reported, which seems to be  
related to the slashes (\ /) in the string.  For example, you do get  
the correct molecule, albeit without control over stereochemistry,  
with smiles:CC=CC=CCCCCCCCCCO

The status line message suggests that Chimera may be processing the  
string incorrectly before sending it to the Web service, but we will  
have to investigate that further and get back to you.  I'll file a bug  
report and put you on the notification list (you will get some  
additional messages about that later).  If it is a limitation of the  
Web server, however, we may not be able to fix it.  In the future, if  
you run into another problem that could be a bug, please use "Help...  
Report a Bug" in the Chimera menu to send us the information -- that  
will automatically include what version of Chimera and type of  
computer you are using, since sometimes those are important.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 27, 2009, at 10:40 AM, George Tzotzos wrote:

> Hi Elaine
>
> I'm using the <open smiles> command as per your instructions (see  
> your message below).
>
> The ligand I'm trying to build is: (10E,12Z)-tetradeca-10,12-dien-1- 
> ol. The SMILES formula I'm using is: C\C=C/C=C/CCCCCCCCCO
>
> What I get is nonanol. The program returns
>
> opened CCCCCCCCCO containing 1 model, 30 atoms, and 1 residues
>
> Obviously, I'm using a different SMILES convention than Chimera.
>
> I'd appreciate you suggestion regarding the SMILES convention, I  
> should be using.
>
> All the best
>
> George
>
> George T. Tzotzos, PhD
> Dept. of Molecular Genetics
> Univ. of Gent, Belgium