That is to say, I just found a mistake in the way the JavaScript version is
working. Looking into that now. Java is OK.
On Fri, Apr 7, 2017 at 12:46 PM, Robert Hanson <[email protected]> wrote:
> ps -- *before I find it*
>
> On Fri, Apr 7, 2017 at 12:42 PM, Robert Hanson <[email protected]> wrote:
>
>> Super. Tell them there is a prize for the first student who finds a
>> mistake in assignment.
>>
>>
>>
>> On Fri, Apr 7, 2017 at 1:52 AM, Pierluigi Quagliotto <
>> [email protected]> wrote:
>>
>>> Dear Bob,
>>>
>>> many thanks for it!
>>>
>>> In this weekend I will try to update my page and make proper test. Once
>>> I will be able to put the page on the production site I will put my student
>>> to make extensive tests, with both simple and complex molecules, to help
>>> you to validate the novel function. I'll let you know when the page will be
>>> ready, just to see it "at work".
>>>
>>> Bye!
>>>
>>> Pierluigi Quagliotto
>>>
>>>
>>> Il 07/04/2017 01:21, Robert Hanson ha scritto:
>>>
>>> This is done.
>>>
>>>
>>> Jmol.___JmolVersion="14.12.0" // 2017-04-06
>>>
>>> new feature: {atom}.chirality
>>> -- uses Cohen-Ingold-Prelog rules to assign R or S to a carbon center
>>> -- ignores sulfur chirality
>>> -- may not fully implement high symmetry cases
>>> -- not fully tested
>>> -- Checked using:
>>>
>>> function checkchiral(m) {
>>> if (m) load @m
>>> background label yellow
>>> color labels black
>>> select _C
>>> label %[atomname]
>>> refresh
>>> var b = {_C}
>>> for (var a in b) {
>>> var c = a.chirality;
>>> print _smilesString + " " + a + c
>>> if (c) {
>>> select a
>>> c = a.atomname + " " + c
>>> label @c
>>> }
>>> }
>>> select *
>>> }
>>>
>>> checkchiral("$(R)-glycidol")
>>> delay 1
>>> checkchiral("$glucose")
>>> delay 1
>>> checkchiral("$(2S,3R)-2,3-oxiranediol")
>>> delay 1
>>> checkchiral("$(S)-2-butanol")
>>> delay 1
>>> checkchiral("$(R)-2-butanol")
>>> delay 1
>>> checkchiral("$(2S,3R)-2,3-butanediol")
>>> delay 1
>>> checkchiral("$(2S,3S)-2,3-butanediol")
>>> delay 1
>>> checkchiral("$(2R,3R)-2,3-butanediol")
>>> delay 1
>>> checkchiral("$(2R,3S)-2,3-butanediol")
>>> delay 1
>>> checkchiral("$1,4-dimethylcyclohexane")
>>> delay 1
>>> checkchiral("$cholesterol") // (3S,8S,9S,10R,13R,14S,17R) and sidechain R
>>>
>>>
>>>
>>>
>>> On Thu, Apr 6, 2017 at 3:41 PM, Pierluigi Quagliotto <
>>> [email protected]> wrote:
>>>
>>>> Dear Bob,
>>>>
>>>> many thanks for your answer.
>>>> I had a look to the paper, but it is very concise, so I would be in
>>>> doubt about how to proceed. If we (I and a young fellowship who should help
>>>> me for the site in next months) can envisage what (and how to do) we will
>>>> let you know some more. Obviously, if this feature will become available in
>>>> JMol/JSMol, this should be nice and also a great improvement for teaching!
>>>>
>>>> I will start to introduce the page I prepared in the production site,
>>>> just to let student to familiarize with the common procedure used to
>>>> approach to chirality determination. If some improvement about chirality
>>>> determination will be available in JMol/JSMol in the future, I will use it
>>>> enthusiastically. In the last two-three years, as long as my site teaching
>>>> site was produced and developed, I observed great improvement in the
>>>> student's ability to comprehend concepts and use them in solving problems,
>>>> so I will try to do all my best to make continuous site improvements, as
>>>> far as I am able to deal with programming.
>>>>
>>>> Many thanks again for the time you dedicate to me,
>>>>
>>>> Bye!
>>>>
>>>> Pierluigi
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> Il 06/04/2017 14:29, Robert Hanson ha scritto:
>>>>
>>>>
>>>>
>>>> On Thu, Apr 6, 2017 at 2:20 AM, Pierluigi Quagliotto <
>>>> [email protected]> wrote:
>>>>
>>>>> Dear All,
>>>>>
>>>>> I prepared a page for students (on my developing server:
>>>>> http://5.135.186.232/STdM/index.php/it/esercizi/esercitarsi-
>>>>> sulla-chiralita),
>>>>> in which they can:
>>>>>
>>>>> 1) write down an organic molecule in JSME
>>>>>
>>>>> 2) submit it to JSmol
>>>>>
>>>>> 3) attribute the Cahn-Ingold-Prelog priority to each group by selecting
>>>>> the first atom of each group which is attached to the Chiral Carbon and
>>>>> clicking on a button that create a label for that atom.
>>>>>
>>>>> 4) reorientate properly the molecule, in order to be able to assign the
>>>>> R / S configuration for chirality.
>>>>>
>>>>> This is enough for me to use in classroom just to show how one should
>>>>> proceed to work on exercises.
>>>>>
>>>>>
>>>>> My question is: Is there a way to obtain priority (by CIP rules) for
>>>>> each group attached to a Chiral Carbon? Is it possible to use some
>>>>> JSmol
>>>>> function(s) to obtain this information?
>>>>>
>>>>>
>>>> ho, ho! No, sorry. Can't do that. But I love the idea. In principal the
>>>> algorithm is not all that difficult.
>>>> https://www.chemcomp.com/journal/chiral.htm Maybe it's time to add
>>>> that...
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>> If the answer is yes, this could help me to modify the page to give the
>>>>> student the chance to explore the correct result by viewing a model
>>>>> with
>>>>> correct priority labelling and also by clicking on a button which
>>>>> activate a function that perform the check.
>>>>>
>>>>>
>>>>> Sorry to bothering you...
>>>>>
>>>>>
>>>>> Bye!
>>>>>
>>>>>
>>>>> Pierluigi Quagliotto
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> Check out the vibrant tech community on one of the world's most
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>>>>> _______________________________________________
>>>>> Jmol-users mailing list
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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
>>>>
>>>>
>>>> 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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>>>>
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>>>
>>> --
>>> Robert M. Hanson Larson-Anderson 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
>>>
>>> ------------------------------------------------------------------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>>>
>>> _______________________________________________
>>> Jmol-users mailing
>>> [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
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>>>
>>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson 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
>>
>>
>
>
> --
> Robert M. Hanson
> Larson-Anderson 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
>
>
--
Robert M. Hanson
Larson-Anderson 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
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