Yes, that's totally true, they are not real molecules. It's just a list of
examples that have been used to test
another source code. The main difference with "real molecules" is that the
atoms are much closer
so I had to decrease the tolerance, and this might be the source of all
problems.
When real molecules and regular distances are involved Jmol gets the right
point group perfectly.
About freezing jmol, if I load this "molecule"
http://144.92.39.89/xavier/symmetry/index.php?symm=D2d
if distance tolerance is set to 0.1 jmol says it's D4h, if it's set to 0.09
it freezes (FF in Mac, Ubuntu and Windows)
I just thought it would be useful to point out the cases where jmol doesn't
seem to work, so that
a possible bug could be found. But, Bob, if you have identified the problem
(atoms too close) and think
that it's not worth the time to fix it that's totally fine with me too.
Thanks for checking this out anyway
Xavier
On Tue, Sep 2, 2008 at 10:39 PM, Dean Johnston <[EMAIL PROTECTED]>wrote:
> 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
>>>>>>>
>>>>>>>
>>>>>>> -------------------------------------------------------------------------
>>>>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>>>>> challenge
>>>>>>> Build the coolest Linux based applications with Moblin SDK & win
>>>>>>> great prizes
>>>>>>> Grand prize is a trip for two to an Open Source event anywhere in the
>>>>>>> world
>>>>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>>>>> _______________________________________________
>>>>>>> Jmol-developers mailing list
>>>>>>> [email protected]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> -------------------------------------------------------------------------
>>>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>>>> challenge
>>>>>> Build the coolest Linux based applications with Moblin SDK & win great
>>>>>> prizes
>>>>>> Grand prize is a trip for two to an Open Source event anywhere in the
>>>>>> world
>>>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>>>> _______________________________________________
>>>>>> Jmol-developers mailing list
>>>>>> [email protected]
>>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>>
>>>>> -------------------------------------------------------------------------
>>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>>> challenge
>>>>> Build the coolest Linux based applications with Moblin SDK & win great
>>>>> prizes
>>>>> Grand prize is a trip for two to an Open Source event anywhere in the
>>>>> world
>>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>>> _______________________________________________
>>>>> Jmol-developers mailing list
>>>>> [email protected]
>>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>>>
>>>>>
>>>>
>>>>
>>>> -------------------------------------------------------------------------
>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>>> challenge
>>>> Build the coolest Linux based applications with Moblin SDK & win great
>>>> prizes
>>>> Grand prize is a trip for two to an Open Source event anywhere in the
>>>> world
>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>>> _______________________________________________
>>>> Jmol-developers mailing list
>>>> [email protected]
>>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>>
>>>>
>>>
>>>
>>> --
>>> 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
>>>
>>> -------------------------------------------------------------------------
>>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>>> challenge
>>> Build the coolest Linux based applications with Moblin SDK & win great
>>> prizes
>>> Grand prize is a trip for two to an Open Source event anywhere in the
>>> world
>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>>> _______________________________________________
>>> Jmol-developers mailing list
>>> [email protected]
>>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>>
>>>
>>
>>
>> --
>> 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
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the
>> world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Jmol-developers mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>>
>>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Jmol-developers mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
--
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
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Jmol-developers mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
