sorry -- got buried during BCCE On Mon, Aug 2, 2010 at 10:51 AM, Otis Rothenberger <[email protected]>wrote:
> Bob, > > JME automatically creates a bromonium ion (and other onium ions) when it > is chemically logical. When this ion is transferred to Jmol, it is > rendered as the Unknown atom, Xx. The problem is really any three > character string ion created by Jmol (e.g. Cl+). I can script around > this, but script around is another term for work around, and I know > that's a term you do not like. Is this problem addressable inside Jmol? > > Shouldn't be a problem.... done. > By the way, I notice that the IU 2D to 3D SMILES site is up again. It > has been down for a while. There has been one significant change. An > unreadable SMILES returns and empty molfile. This allows graceful error > message scripting. > > The NIH SMILES translator, a new discovery for me, is incredible: > > http://cactus.nci.nih.gov/translate/ > > Great. Why don't you see if you can contact them and suggest they give us a direct link to the 3D mol file. Also check that stereochemistry for bonds and atoms is working there. > I can pass a Jmol SMILES to it directly and get the 3d molfile return, > but an intervening NIH page prevents direct loading into Jmol. Still the > site produces a quality 2D to 3D translation with lightning speed. > > The ability to keep track of a stereo SMILES in an evolving Jmol model > kit model was a wonderful addition to Jmol. > > Otis > > -- > Otis Rothenberger > chemagic.com > > > > > > ------------------------------------------------------------------------------ > The Palm PDK Hot Apps Program offers developers who use the > Plug-In Development Kit to bring their C/C++ apps to Palm for a share > of $1 Million in cash or HP Products. Visit us here for more details: > http://p.sf.net/sfu/dev2dev-palm > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- 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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