Excellent. That works.
Related to the mf array this leads to, what’s the best way to hand a JmolScript
array to a page JavaScript function? The only way I know how to do this is with
Message Callback. Is there a more direct way?
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Jun 30, 2016, at 10:33 AM, Robert Hanson <hans...@stolaf.edu> wrote:
>
> My mistake. The way to do this is
>
> n = {*}.molecule.max
>
> On Thu, Jun 30, 2016 at 9:57 AM, Philip Bays <pb...@saintmarys.edu
> <mailto:pb...@saintmarys.edu>> wrote:
> 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
>> <mailto: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 <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/>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> 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
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> 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
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>>> everyone, including kids. Get more information and register today.
>>> http://sdm.link/attshape_______________________________________________
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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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>
> Philip Bays
> Emeritus Professor of Chemistry
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu <mailto:pb...@saintmarys.edu>
>
>
>
> ------------------------------------------------------------------------------
> 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.
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> _______________________________________________
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> <https://lists.sourceforge.net/lists/listinfo/jmol-users>
>
>
>
>
> --
> 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_______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
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