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
>>>
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
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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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>
> --
> 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
> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
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> ------------------
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> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
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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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