yep. Thanks
On Apr 12, 2010, at 2:34 PM, Robert Hanson wrote:
> 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 <[email protected]> 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 <[email protected]>
>> 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: [email protected]
>> Message-ID:
>> <[email protected]>
>> 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
>> [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
>> ------------------------------------------------------------------------------
>> 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
>> [email protected]
>> 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
> [email protected]
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> [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
> ------------------------------------------------------------------------------
> 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
> [email protected]
> 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
[email protected]
------------------------------------------------------------------------------
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
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
