ps -- *before I find it*
On Fri, Apr 7, 2017 at 12:42 PM, Robert Hanson <hans...@stolaf.edu> 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 <
> pierluigi.quaglio...@unito.it> 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 <
>> pierluigi.quaglio...@unito.it> 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 <
>>> pierluigi.quaglio...@unito.it> 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
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
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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
>>>
>>>
>>>
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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
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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
>
>
--
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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