Ok, with a little help from Peter Ertl, I think I understand the JME's 4 stereo bond rotation. Maybe this was all resolved on the group exchange previously, but I missed it if it was published.
The four stereo bond rotation will only work if it is relevant to two attached chiral carbon atoms. For example, it works for: http://chemagic.com/web_molecules/script_page_large.aspx?jme=7%206%20C%208.88%20-5.32%20C%204.03%20-5.32%20C%206.46%20-6.72%20Br%205.24%20-3.22%20C%207.67%20-4.62%20C%205.24%20-4.62%20C%206.46%20-5.32%201%205%201%202%206%201%203%207%201%204%206%201%205%207%201%206%207%201 The above uses Bob's newly invented email transfer of models via query string. I just love it! On our site, the model loads into Jmol. On the JME Draw screen, you can Depict it and play with it in JME. Sorry about not removing the hydrogens in the Depict. That's doable, but it's a bit buggy yet, so I'm still working on it. I should note, that the above structure was created flat, so the sterechemistry represents what Jmol's jmeFile load decided to do with this flat structure. If you cannot load the above structure it is 2-bromo-3-methylpentane, which Jmol renders as (2S,3S)-2-bromo-3-methylpentane, at least on my system. Otis -- Otis Rothenberger chemagic.com ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
