[Chimera-users] reading SMILES description into Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 1 09:04:14 PST 2012

Hi Boaz,
You can just use the command line, for example:

open smiles:CC1=CC=C(C=C1)S(=O)(=O)[O-]

I'm thinking it may be a mistake that SMILES shows up as a file type in the "Open File" dialog.

 The only other place I can think of is in Build Structure (under Tools... Structure Editing), where the Start Structure section includes a SMILES option.  In that case you would just type or paste in the SMILES string in the indicated field.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 1, 2012, at 7:08 AM, Boaz Shaanan wrote:

> Hi,
> I'm trying to read a small molecule for which I have a SMILES description into Chimera. I selected 'smiles' from the input options but it's not clear to me how to proceed. Do I have to generate a text file with the smiles description in it? do I paste the smiles description in the file name line? or what?
> Thanks for your help.
>                      Boaz
> Boaz Shaanan, Ph.D.                                         
> Dept. of Life Sciences                                      
> Ben-Gurion University of the Negev                          
> Beer-Sheva 84105                                            
> Israel                                                      
> E-mail: bshaanan at bgu.ac.il
> Phone: 972-8-647-2220  Skype: boaz.shaanan                  
> Fax:   972-8-647-2992 or 972-8-646-1710    
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