Bob: I am really impressed with this capability!! However, I have a couple of
issues on the mac side of things.
When I use Firefox, Camino, or SeaMonkey I get an error message when loading
JME: The structure you have in there will not load. But I can use them to
correctly generate structures and load them into Jmol.
With Safari, I can use your structure or my own and get the Jmol structure, but
in this case none of the wedge or dashed bonds in the JME structure show
connections in the Jmol structure. They are apparently there because nothing
goes flying off into space on minimization, but the bonds are not visible,
And in some cases there are extra bonds to hydrogens (three membered rings
containing hydrogen.)
Phil
On Apr 12, 2010, at 11:38 AM, Robert Hanson wrote:
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
>
> now smoothly integrates JME with Jmol. Still two applets -- just shows how to
> use JME as a quick input mechanism. Also uses Jmol to read the files that JME
> can then display. Question: does JME allow direct file reading, or it is only
> reading strings of data? If the latter, well, now it reads files.
>
> Bob
>
>
> On Sun, Apr 11, 2010 at 5:03 PM, Greeves, Nick <ngree...@liverpool.ac.uk>
> wrote:
>
> Yes, very cool and easy to use, perhaps too easy?
>
> My concern is the limitations of the minimisation which will lead to high
> energy "minima". e.g. Cis decalin becomes chair-boat instead of chair-chair,
> biphenyl is flat, simple amides are not planar. This is not Jmol's fault per
> se but could be misleading.
>
> Otherwise works nicely.
>
>
> All the best
> Nick
> --
> 3D Organic Animations http://www.chemtube3d.com
> Tel: +44 (0)151-794-3506 (3500 secretary)
>
>
> Subject: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D
> To: jmol-users@lists.sourceforge.net
> Message-ID:
> <o2sba9c0bd61004102152r2848f768x43d726fab5e02...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> OK! Here we go! Super simple 2D to 3D.
>
> The JME-Jmol connection has gone unused for too long. With today's 12.0.RC5
> addition of reading bond stereochemistry, Jmol now does a pretty decent job
> of translating 2D into 3D -- admittedly this is not going to solve all
> problems, but give it a try:
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
>
> Cool, eh?
> ------------------------------------------------------------------------------
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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
> ------------------------------------------------------------------------------
> 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
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J. Philip Bays
Professor of Chemistry
Department of Chemistry and Physics
Saint Mary's College
Notre Dame, IN 46556
(574) 284-4663
pb...@saintmarys.edu
------------------------------------------------------------------------------
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
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