Otis:
I confirm your observation using Safari. But in Firefox, n = 2. Safari can’t
count?
> On Jun 30, 2016, at 12:29 AM, Otis Rothenberger <osrot...@icloud.com> wrote:
>
> Bob,
>
> Go to your test2.htm page and load hexanal from PubChem (not Resolver). Enter
> model kit mode and use delete bond to break hexanal into 3 parts. Exit model
> kit mode and use the console to enter n={*}[0].molecule;show n. You’ll get n
> = 1. As an aside n={*}[-1].molecule;show n yields n = 3
>
> Maybe this is a Safari thing. I worked on this some more today, and I’m
> seeing erratic n=1 in other cases not involving obvious presence of partial
> charge.
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org <mailto:o...@chemagic.org>
> http://chemagic.org
>
>> On Jun 29, 2016, at 10:53 PM, Robert Hanson <hans...@stolaf.edu
>> <mailto:hans...@stolaf.edu>> wrote:
>>
>> I still don't get what the problem is.
>>
>> On Wed, Jun 29, 2016 at 2:21 PM, Otis Rothenberger <osrot...@icloud.com
>> <mailto:osrot...@icloud.com>> wrote:
>> Bob,
>>
>> I should gave given you two more data points on the PubChem issue. I'm sure
>> you know the first: If PubChem comes in with charges, these charges are
>> appended to the Jmol molfile extraction.
>>
>> Second, If a Jmol extracted molfile containing these PubChem charges is
>> loaded into Jmol, this load carries with it the {*}[0].molecule problem.
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.org <mailto:o...@chemagic.org>
>> http://chemagic.org <http://chemagic.org/>
>>
>> On Jun 29, 2016, at 8:52 AM, Robert Hanson <hans...@stolaf.edu
>> <mailto:hans...@stolaf.edu>> wrote:
>>
>>> I'll check on what's up with the partial charges. No effect on
>>> {molecule=1}.find("MF"), I'm fairly certain.
>>>
>>> On Wed, Jun 29, 2016 at 8:50 AM, Robert Hanson <hans...@stolaf.edu
>>> <mailto:hans...@stolaf.edu>> wrote:
>>> {*}.find("MF") will report the MF you want. No need to go through the
>>> propery. But I hear you. Yes, probably moleculeInfo should do that. It's a
>>> simple fix.
>>>
>>>
>>>
>>> On Wed, Jun 29, 2016 at 1:35 AM, Otis Rothenberger <osrot...@icloud.com
>>> <mailto:osrot...@icloud.com>> wrote:
>>> Bob,
>>>
>>> First, AAARGH! Finally.
>>>
>>> Here’s what messes up [n = {*}[0].molecule;show n] in Jmol - Otis.htm and
>>> Test2.htm
>>>
>>> PubChem provides SDF's with partial charges and without partial charges.
>>> Actually, they are always there, but some are listed
>>>
>>> > <PUBCHEM_MMFF94_PARTIAL_CHARGES>
>>> 0
>>>
>>> If the PubChem file actually lists non-zero charges, then cutting the
>>> resulting molecule up in Jmol makes [n = {*}[0].molecule;show n] behave
>>> erratically.
>>>
>>> I load by default from PubChem, and a McLafferty Rearrangement model kit
>>> problem using hexanal that I was setting up started this whole email chain
>>> with the mf problems. I just kept working with PubChem hexanal while I was
>>> trying to find the “funky” behavior on my page. It was just dumb luck that
>>> I noticed the PubChem relationship.
>>>
>>> OK, now that I can use n = {*}[0].molecule, I need to get the mf array over
>>> to JavaScript. What’s the best route - message callback?
>>>
>>> Finally, it seems to me that if CH2 is in the Jmol window, then a simple
>>> extraction of mf should be CH2 - not CH4. I’m just saying. This, of course,
>>> is a small molecule guy’s opinion!
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.org <mailto:o...@chemagic.org>
>>> http://chemagic.org <http://chemagic.org/>
>>>
>>>
>>> ------------------------------------------------------------------------------
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>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Larson-Anderson Professor of Chemistry
>>> St. Olaf College
>>> Northfield, MN
>>> http://www.stolaf.edu/people/hansonr <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
>>>
>>>
>>>
>>>
>>> --
>>> Robert M. Hanson
>>> Larson-Anderson Professor of Chemistry
>>> St. Olaf College
>>> Northfield, MN
>>> http://www.stolaf.edu/people/hansonr <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
>>>
>>> ------------------------------------------------------------------------------
>>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
>>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
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>>
>> ------------------------------------------------------------------------------
>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
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>>
>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> St. Olaf College
>> Northfield, MN
>> http://www.stolaf.edu/people/hansonr <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
>>
>> ------------------------------------------------------------------------------
>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
>> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
>> present their vision of the future. This family event has something for
>> everyone, including kids. Get more information and register today.
>> http://sdm.link/attshape_______________________________________________
>> <http://sdm.link/attshape_______________________________________________>
>> Jmol-users mailing list
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>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
> ------------------------------------------------------------------------------
> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
> Francisco, CA to explore cutting-edge tech and listen to tech luminaries
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> http://sdm.link/attshape_______________________________________________
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Philip Bays
Emeritus Professor of Chemistry
Saint Mary's College
Notre Dame, IN 46556
pb...@saintmarys.edu
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