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

Robert Hanson hansonr at stolaf.edu
Fri May 28 07:41:28 PDT 2010

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,


I note that


gives the same result. Far as I can tell they require


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

Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
phone: 507-786-3107

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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