Otis -- by the way, I made the minimization "silent" automatically, so you
won't see the jittering in the latest version of Jmol. Are you able to go 3D
to 2D? I'm not finding that....
I suggest a title="..." attribute in those MM Load and MO Load options. I
have no idea what MM and MO refer to, but I'm guessing that a quick tip
would explain it. That goes for most of the other links. People like to
hover over a link and get a clue as to what it means. Best way to learn --
better than "just click it" in my opinion.
Bob
On Wed, Apr 14, 2010 at 11:20 AM, Otis Rothenberger
<osrot...@chemagic.com>wrote:
> 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
>
>
>
>
>
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--
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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