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

Eric Pettersen pett at cgl.ucsf.edu
Tue Sep 29 14:08:24 PDT 2009

On Sep 28, 2009, at 8:55 AM, Elaine Meng wrote:

> 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

It turns out that the web service at Indiana University wasn't  
handling SMILES with forward slashes correctly, only translating the  
string after the last slash.  They have fixed that bug and Chimera  
will now get the right structure for your SMILES string.


> 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
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