On Fri, Aug 28, 2009 at 5:29 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

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:
<http://www.cgl.ucsf.edu/chimera/download.html#snapshots>

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):
<http://www.cgl.ucsf.edu/chimera/1.4_b28596/docs/relnotes/snapshot.html>

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