Re: [Jmol-users] Script error : Partial charges computation fails after minimization

[Paul P. <pau...@gm...>]

Dear Otis,
Following your advices, I’ve finally made it working.
It introduced another strange bug where an extra bond picking event was sometimes auto-generated after the reload, but I circumvented it also by disabling bond picking.
Final result can be seen (« En français ») at http://www.librairiedemolecules.education.fr/outils/scribmol/scrib.html <http://www.librairiedemolecules.education.fr/outils/scribmol/scrib.html> 
Thanks again for your help,
Paul


> Le 22-01-2018 à 11:48, Paul PILLOT <pau...@gm...> a écrit :
> 
> Thanks Otis,
> I get it! I also thought there was a caching process involved in this behaviour. Reloading makes sense to start these computations anew. I will try your workaround and let you know of my whereabouts.
> 
> Paul
> 
>> Le 22-01-2018 à 11:03, Otis Rothenberger <osr...@gm... <mailto:osr...@gm...>> a écrit :
>> 
>> Paul,
>> 
>> Thanks for the kind words!
>> 
>> The main thing I should have mentioned is that I invoke that reload just prior to my calculation on new partial charges. When Bob added the partial charges to Jmol SDF generation, I found that I had to erase them before recalculating partial charge after atom editing.
>> 
>> I assume that these charges are added to the Jmol SDF when you use “calculate partialCharge”, and  this was nice addition to Jmol. Unfortunately, the SDF charges affected subsequent charge calculation after atom editing. Consequently, I simply erase them by the previously discussed erase/reload.
>> 
>> Otis
>> 
>> —
>> Otis Rothenberger
>> http://CheMagic.ORG <http://chemagic.org/>
>> 
>> On Jan 22, 2018, at 10:49 AM, Paul PILLOT <pau...@gm... <mailto:pau...@gm...>> wrote:
>> 
>>> Thanks Otis,
>>> your site is such a valuable source of information to me!
>>> I see that what I want to achieve works flawlessly on your website.
>>> Unfortunately, I am not able to reproduce it by decomposing the individual Jmol script calls that your website makes to correctly compute partial charges.
>>> I’ll continue to investigate this further.
>>> Best regards,
>>> Paul 
>>> 
>>>> Le 22-01-2018 à 10:17, Otis Rothenberger <osr...@gm... <mailto:osr...@gm...>> a écrit :
>>>> 
>>>> One more thought Paul,
>>>> 
>>>> Over the years, I encountered many of the issue related to “modelkiting” with Jmol. All of the virtual model kit’s code is in the HTML page. My scripting is a bit chaotic, but it might be useful to you:
>>>> 
>>>> http://chemagic.org/molecules/mini.html <http://chemagic.org/molecules/mini.html>
>>>> 
>>>> Otis
>>>> 
>>>> —
>>>> Otis Rothenberger
>>>> http://CheMagic.ORG <http://chemagic.org/>
>>>> 
>>>> On Jan 22, 2018, at 9:29 AM, Paul PILLOT <pau...@gm... <mailto:pau...@gm...>> wrote:
>>>> 
>>>>> Thanks Otis,
>>>>> it indeed corrects the error!
>>>>> 
>>>>> 
>>>>> Now that it’s working, I am encountering another problem: the partial charges computation doesn’t change (or inconsistently) after I have replaced an oxygen by a nitrogen for example, except for connected hydrogens which display a 0 value (?).
>>>>> 
>>>>> 
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