oops -- ok. That fix will be uploaded within the hour. On Fri, May 21, 2010 at 8:27 AM, Otis Rothenberger <[email protected]>wrote:
> Bob, > > Needless to say, I'm heavy into playing with this already. One problem on > my end: The minimize command by itself seems to be broken. This is on a > fresh page load prior to "set picking dragMinimize." > > Harping on a Point: As chemists, the model kit was our first educational > touch of intimacy with molecules. It was one of the components of our > education that turned us on to chemistry - our own Maria Montessori thing. I > agree. This is a wonderful addition to Jmol. > > Otis > > > On 5/21/2010 9:01 AM, Robert Hanson wrote: > > First - I should point out that this required almost no coding -- we > already had minimization and bindings; this just added a couple of new > options and a bit of stitching. I'm not sure "set picking dragMinimize" is > quite the right way to do this, but it's OK for this week. > > Ah, yes, what to do with it?? > > My organic class and I were reviewing for the final last night. I popped up > methylcyclohexane and started quizzing them in relation to gauche > interactions and conformations. It was quite fun to just tug on the molecule > to switch from equatorial to axial or from chair to twist-boat. I think the > energies in UFF might be meaningless, but the ease of manipulating the model > this way was great fun and way faster than anything else I've ever used -- > no setup, no special page, just pull in the molecule and start tugging. > > It would have been especially nice to just be able to hover over an atom or > bond and delete it or modify it. I have a hunch that if you added to this a > simple model building kit (mostly just a few context-sensitive drop-down > menus that would appear when you hover over an atom, I think), it would > pretty much take care of anything I would need in teaching about structure > in relation to conformations of cyclohexane -- except for a couple of pages > like http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm, > which is based on a more refined optimization. (Note that you can just > drag-and-drop a Spartan file from your hard drive in there, and it will > display its full energy profile.) > > In addition, since now we can test for matches to specific conformations, > already it would be simple enough to write a blank-slate page that would ask > the student questions like, "Shown below is 2-methylcyclohexane. By pulling > on atoms, change this model to one that is a chair conformation that has an > axial methyl group." -- and then test for that using the COMPARE function. I > think it opens up some interesting possibilities that we haven't had before. > > I was thinking before that it has "questionable pedagogic value" because > obviously you can't really do this sort of thing with a molecule, but as I > think about it more, you can't just click on an atom in a real molecule and > invert stereochemistry at that center, either! So every "model kit" has its > deceit. > > One wonders, though, to a certain extent, does a molecule "respond" to at > least minor distortions this way? I was intrigued by how the whole molecule > responded when I yanked hard on an H atom. I honestly had never thought of > that before, and only had thought of interactions such as that as being far > more localized. But as I play with it and think about the forces involved, I > have to say I think there's something there. > > Still pondering this. > > 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 > > > ------------------------------------------------------------------------------ > > > > > _______________________________________________ > Jmol-users mailing > [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users > > > -- > Otis Rothenbergerchemagic.com > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > 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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