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
http://chemagic.org
> On Jun 29, 2016, at 10:53 PM, Robert Hanson <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
>>
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>> Attend Shape: An AT&T Tech Expo July 15-16. Meet us at AT&T Park in San
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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
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