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?
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/ 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
