It's been a VERY good week. First we get a working model kit for Jmol, and now SMILES to 3D:
>From the application or SIGNED applet: load SMILES "CC1C(C)c...@h]coc(=O)C1" or, simply, load $CC1C(C)c...@h]coc(=O)C1 ($ indicates SMILES, like = indicates PDB) and print load("$CCCC") or Var x = load("$CCCC") Need I say more? :) see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?USEDSIGNED Yes, I suppose I do need to say more. This uses a web service at Indiana University http://cheminfo.wikispaces.com/smi23d that appears to use PCMODEL for its converter. The idea is similar to the way "=xxxx" goes to the RCSB site. The implementation is not entirely reliable, at least I noticed that it did double-bond stereochemistry wrong for some simple conjugated systems. For example: F/C=C/C=C\C gives the expected E,Z configuration, but F/C=C/C=C/C ALSO gives that configuration. To get E,E you have to use F/C=C/\C=C/C But that's not a valid SMILES string, as far as I know. So something is amiss there. And certain atoms such as [Na] aren't recognized. Also, formal charge is not recognized, for example [C+] doesn't result in fewer H atoms. C60's SMILES string didn't work. So it's definitely not a perfect solution. But it's a start. We need to do more testing on this, of course. Bob -- 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
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