Re: [Chimera-users] Using Chimera to read SMILES string into structure
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 -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr 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
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
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Elaine Meng -
Robert Hanson