[Chimera-users] Problem building 3D structure from smile text ...(Solved. Thanks)

Sergio Garay sergio.alberto.garay at gmail.com
Sat Aug 29 05:36:12 PDT 2009

Thank tou Alaine. The new chimera version works perfect!

On Fri, Aug 28, 2009 at 5:29 PM, Elaine Meng <meng at 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
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco

Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221
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