The test set is quite artificial, but it's designed to be "hard", not
realistic. I think it was designed as more of a worst case to check the
robustness of the brute force algorithm. It might be more interesting
(useful?) to come up with a diverse set of real, but not idealized,
molecules and see if Jmol will identify the correct (ideal) point group
given a high enough tolerance.
Dean
On Tue, Sep 2, 2008 at 2:15 PM, Robert Hanson <[EMAIL PROTECTED]> wrote:
> Xavier,
>
> When I looked at that site, I thought the molecules that were being missed
> were not very precise models, or I think were not very representative of
> real molecules. Is that a correct characterization?
>
> For example, C7 is not supported. Do you have an actual molecular example
> of that?
>
> So before you conclude that there's a real problem, I suggest using real
> molecules. :)
>
>
> The Mac problem -- just give me one specific example of the problem, and
> others can try it on their Macs to see what they can determine.
>
> Bob
>
>
>
> On Tue, Sep 2, 2008 at 10:17 AM, Xavier Prat-Resina <[EMAIL PROTECTED]>wrote:
>
>> Bob,
>>
>> regarding the point group symmetry, I'm still observing the same problems
>> I reported
>> few weeks ago.
>> http://144.92.39.89/xavier/symmetry/
>> It's true that in Mac Jmol freezes and in Windows it doesn't (IE/FF), but
>> jmol doesn't
>> find all the symmetry operations the molecules have.
>>
>> Xavier
>>
>>
>> On Sat, Aug 30, 2008 at 7:03 AM, Dean Johnston <[EMAIL PROTECTED]>wrote:
>>
>>> Thanks - works beautifully - and now has a draw pointgroup button. (It
>>> still doesn't work with Safari for some reason, though - I haven't had time
>>> to track that down.)
>>>
>>> Dean
>>>
>>>
>>> On Sat, Aug 30, 2008 at 9:16 AM, Robert Hanson <[EMAIL PROTECTED]>wrote:
>>>
>>>> OK, that's fixed. It was a problem with my uploading -- My Filezilla
>>>> script hadn't been updated to include the additional symmetry class files.
>>>> So although JmolApplet.jar worked, JmolApplet0.jar didn't. Same for signed.
>>>>
>>>> Dean, your page is working now -- it's such a nice page, can you add a
>>>> button for
>>>>
>>>> draw pointgroup
>>>>
>>>> as well?
>>>>
>>>> Bob
>>>>
>>>>
>>>>
>>>> On Fri, Aug 29, 2008 at 10:23 PM, Dean Johnston <[EMAIL PROTECTED]>wrote:
>>>>
>>>>> No, it's freezing for me as well. It's pulling the most recent version
>>>>> of Jmol from http://chemapps.stolaf.edu/jmol/docs/examples-11/, so it
>>>>> seems to be something that's changed in Jmol. I've updated the page so
>>>>> that
>>>>> it doesn't try to check the point group until you push the *Check
>>>>> Point Group* button. That's when it freezes for me.
>>>>>
>>>>> The code for this page has lots of unecessary junk hanging around since
>>>>> it was adapted from the "Gallery" page. The molecules are defined in
>>>>> individual Javascript (JSON) files. I read in the Javascript file using
>>>>> *XMLHttpRequest* and then pass the molecule to Jmol as an inline data
>>>>> file. If you want molecules that you can check, go to
>>>>> http://symmetry.otterbein.edu/gallery_old/molecules/moldata.xml. That
>>>>> should give you a listing of all the molecules in that directory that are
>>>>> xml files. Prototype.js (http://www.prototypejs.org/) is Javascript
>>>>> framework that makes some AJAX (like XMLHttpRequest and DOM manipulation)
>>>>> stuff a bit easier.
>>>>>
>>>>> Dean
>>>>>
>>>>>
>>>>> On Fri, Aug 29, 2008 at 10:20 PM, Robert Hanson <[EMAIL PROTECTED]>wrote:
>>>>>
>>>>>> Dean, is http://symmetry.otterbein.edu/pgtest/ working for you? It
>>>>>> seems frozen for me. Models show up but cannot be rotated. I can't figure
>>>>>> out what is wrong.
>>>>>>
>>>>>> Also, how does this page work? What is prototype.js? Where do the
>>>>>> molecules come from?
>>>>>>
>>>>>> Bob
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Robert M. Hanson
>>>>>> Professor of Chemistry
>>>>>> St. Olaf College
>>>>>> Northfield, MN
>>>>>> http://www.stolaf.edu/people/hansonr
>>>>>>
>>>>>>
>>>>>> 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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>>>>>
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>>>>
>>>>
>>>> --
>>>> Robert M. Hanson
>>>> Professor of Chemistry
>>>> St. Olaf College
>>>> Northfield, MN
>>>> http://www.stolaf.edu/people/hansonr
>>>>
>>>>
>>>> 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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>>>
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>>
>>
>> --
>> Xavier Prat-Resina
>> Research Associate
>> Journal of Chemical Education and University of Wisconsin
>> 209 N. Brooks St. Madison, WI 53715-1116
>>
>> Tel: 608 8901702 // Fax: 608 2627145
>> e-mail: xavier ( ) chem.wisc.edu ; skype: xavierprat
>> http://x.prat.resina.googlepages.com
>>
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>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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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>
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