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

[Elaine Meng]

Dear Bob,
Since the interchange you found on the archive, I haven't spent time testing the smi23d service in any systematic way.   It sounds like you have looked into this carefully, and I don't doubt your results.   Probably their parser does not handle certain complexities of SMILES.

My impression has been that it can be very useful for one-off, supervised use (i.e. where the user visually verifies the result).   What kinds of errors have you found?  Z/E isomerism, or also R/S?  I tried a simple L-alanine vs. D-alanine test which turned out OK.

I don't know too many details about the protocol, but I believe it was also applied to generate the structures in the Pub3D database and is described briefly (only 1-2 sentences though) in this paper:

Userscripts for the Life Sciences
Egon L Willighagen et al.
BMC Bioinformatics 2007, 8:487doi:10.1186/1471-2105-8-487
http://www.biomedcentral.com/1471-2105/8/487

... but alas, this doesn't say much more than what you get by following the links from the smi23d webpage already linked to your jmol page.

In the past I have contacted Drs. David Wild (the last author on the above paper) and Rajarshi Guha (who was the main developer, I believe, but has changed labs, see http://www.rguha.net/ ) regarding this service.

I'd be interested in hearing more about your findings, opinions, and/or if anything new happens.  You can e-mail just me if it doesn't seem suitable for the chimera-users list.
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 May 28, 2010, at 7:41 AM, Robert Hanson wrote:

> Elaine, I picked up this thread off the web archives. I've just implemented reading SMILES into Jmol (http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm), but I'm pretty dissatisfied with that IU service. Do you know what they are really doing for that? For example, in that one you have there, 
> 
> C\C=C/C=C/CCCCCCCCCO
> 
> I note that
> 
> C\C=C/C=C\CCCCCCCCCO
> 
> gives the same result. Far as I can tell they require
> 
> C\C=C//C=C\CCCCCCCCCO
> 
> which as far as I can tell is invalid SMILES. At least, Daylight's DEPICT thinks it is invalid.
> 
> It has also made several mistakes with relatively simple stereochemistry that I have tried. 
> 
> Is this your experience as well?
> 
> Bob Hanson
> principal developer, Jmol