Phil, this is probably just a caching problem within your browsers. I've
been uploading revised versions all weekend long, and this sounds a lot like
what the capabilities were a few days ago. I just added the capability to
load the structure there this morning. Yesterday when you clicked on the
image you got a blank JME window; today you should see the structure. It's
working fine on my Mac using Safari or Firefox.
Bob
On Mon, Apr 12, 2010 at 12:05 PM, Philip Bays <pb...@saintmarys.edu> wrote:
> 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?
>>
>> ------------------------------------------------------------------------------
>> 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
>>
>
>
>
> --
> 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
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
> 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
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> 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
------------------------------------------------------------------------------
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
