[Chimera-users] Problem building 3D structure from smile text ...

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 28 13:29:26 PDT 2009

Hi Sergio,
Normally if you want to report an error it is best to use "Help...  
Report a Bug" in the Chimera menu since that would automatically  
include information about your computer and Chimera version, and let  
you attach files.

However, in this case I can immediately see the problem:  you need a  
newer version of Chimera!

You would need a version from July 3 or later, for example the August  
20 snapshot:

Explanation:  The SMILES -> 3D structure conversion is done by a Web  
server provided by a group at Indiana University, and a few months  
ago they changed how this service is accessed.  It was necessary to  
change Chimera to use the new, updated service.

I tested the following command in the snapshot version just now, and  
it worked fine:

open smiles:N[C@@H](C)C(=O)O

Using this command is the same as entering the SMILES in the Build  
Structure dialog.  I also checked doing it that way.

I think you will be pleasantly surprised to see the many improvements  
we have made in Build Structure and in other tools, and the many new  
features that have been added to Chimera!

Improvements between 1.3 and the snapshot (and you were using a  
version older than 1.3):

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

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