Re: [Jmol-users] R: Re: Jmol 14.12.1 released -- R/S chirality

2017-04-10 Thread Pierluigi Quagliotto 

Il 09/04/2017 21:16, pinostricc...@alice.it ha scritto:
Great job, Bob. Really. I will implement it on my website for my 
students to use.

Sometime imagining molecules in 3D is not that easy :)
@Pierluigi. I was referring to your pages too with my compliment
Pino

Messaggio originale
Da: hans...@stolaf.edu
Data: 9-apr-2017 14.55
A:
"jmol-users@lists.sourceforge.net"
Ogg: Re: [Jmol-users] Jmol 14.12.1 released -- R/S chirality

I will release another version of Jmol later today that has been
pretty heavily validated using some excellent  extreme examples
provided by Mikko Vainio that caught a couple of bugs.

On Sun, Apr 9, 2017 at 3:46 AM, Pierluigi Quagliotto
> wrote:

Many thanks, Bob!

Bye!

Pierluigi



Il 08/04/2017 03:54, Robert Hanson ha scritto:


https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.12/Jmol%2014.12.1/




Jmol.___JmolVersion="14.12.1"

bug fix: NBO update
bug fix: JavaScript bug - missing Math.signum(f) - causes
{atom}.chirality to not work in JSmol

JmolVersion="14.12.0" // 2017-04-06

new feature: {atom}.chirality
  -- also SELECT chirality = 'R'# or SELECT chirality != ""
  -- uses Cahn-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



-- 
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

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Dear all,

the page I was started to draw about chirality and that inspired Bob to 
develop the chirality recognition functions in JMol is now ready on my 
site at the address:


http://www.iorgchem.unito.it/index.php/en/exercises/practice-on-chirality

Every suggestion / criticism is welcome.

Please note that student should learn the procedure by simply following 
the instructions reported just above the JSME /JSMol panel.


The button Reset was inserted to reset the status of the label 
background after the first check of the answer, since a yellow 
background would be still present when a new trial is done. The student 
that made a mistake can start again without showing a yellow background 
for the label he is introducing on the chiral carbon. The  yellow 
background is intended  for the final "correct" answer only.


Bye,

Pierluigi

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Re: [Jmol-users] R: Re: Jmol 14.12.1 released -- R/S chirality

2017-04-10 Thread Pierluigi Quagliotto 

Many thanks, Pino!

If you like it, my page is now online on the production site at: 
http://www.iorgchem.unito.it. The page is in the menu Esercizi ---> 
Esercitarsi sulla Chiralità.


The page was now updated and the scope is to make students to follow the 
full path:


1) assign the labels to the chiral carbon, and to the 4 substituents.

2) orientate the molecule in the proper way

3) assign the chirality by selecting the chiral carbon and substituting 
the label C with R o S by clicking on the R or S button


4) check the chirality with the button "Controlla Chiralità"

At the present moment the page is intended to work for molecules having 
only one chiral carbon. I should write some function to manage more 
carbons (i.e the typical example of the cholesterol, should be a nice 
test!) by taking action on each as a separate case. If I will have some 
problem in managing this situation (it is not clear to me yet how to 
do...) I will ask you!


for all who are interested into it, the English version will be ready in 
a matter of minutes since I will present it to my student in less than 2 
hours!


 if someone has suggestions or find some bug, please let me know.


Bye! And happy JMol-iing with this novel feature!

Pierluigi

Il 09/04/2017 21:16, pinostricc...@alice.it ha scritto:
Great job, Bob. Really. I will implement it on my website for my 
students to use.

Sometime imagining molecules in 3D is not that easy :)
@Pierluigi. I was referring to your pages too with my compliment
Pino

Messaggio originale
Da: hans...@stolaf.edu
Data: 9-apr-2017 14.55
A:
"jmol-users@lists.sourceforge.net"
Ogg: Re: [Jmol-users] Jmol 14.12.1 released -- R/S chirality

I will release another version of Jmol later today that has been
pretty heavily validated using some excellent  extreme examples
provided by Mikko Vainio that caught a couple of bugs.

On Sun, Apr 9, 2017 at 3:46 AM, Pierluigi Quagliotto
> wrote:

Many thanks, Bob!

Bye!

Pierluigi



Il 08/04/2017 03:54, Robert Hanson ha scritto:


https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.12/Jmol%2014.12.1/




Jmol.___JmolVersion="14.12.1"

bug fix: NBO update
bug fix: JavaScript bug - missing Math.signum(f) - causes
{atom}.chirality to not work in JSmol

JmolVersion="14.12.0" // 2017-04-06

new feature: {atom}.chirality
  -- also SELECT chirality = 'R'# or SELECT chirality != ""
  -- uses Cahn-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



-- 
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 list
Jmol-users@lists.sourceforge.net

https://lists.sourceforge.net/lists/listinfo/jmol-users




--
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 list Jmol-users@lists.sourceforge.net

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

--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot

Re: [Jmol-users] R: Re: Jmol 14.12.1 released -- R/S chirality

2017-04-09 Thread Robert Hanson 
I need to get you a version that has alkynes fixed. I think what is up
there now does not have that.

On Sun, Apr 9, 2017 at 2:16 PM, pinostricc...@alice.it <
pinostricc...@alice.it> wrote:

> Great job, Bob. Really. I will implement it on my website for my students
> to use.
> Sometime imagining molecules in 3D is not that easy :)
> @Pierluigi. I was referring to your pages too with my compliment
> Pino
>
> Messaggio originale
> Da: hans...@stolaf.edu
> Data: 9-apr-2017 14.55
> A: "jmol-users@lists.sourceforge.net"
> Ogg: Re: [Jmol-users] Jmol 14.12.1 released -- R/S chirality
>
>
> I will release another version of Jmol later today that has been pretty
> heavily validated using some excellent  extreme examples provided by Mikko
> Vainio that caught a couple of bugs.
>
> On Sun, Apr 9, 2017 at 3:46 AM, Pierluigi Quagliotto <
> pierluigi.quaglio...@unito.it> wrote:
>
>> Many thanks, Bob!
>>
>> Bye!
>>
>> Pierluigi
>>
>>
>>
>> Il 08/04/2017 03:54, Robert Hanson ha scritto:
>>
>> https://sourceforge.net/projects/jmol/files/Jmol/Version%201
>> 4.12/Jmol%2014.12.1/
>>
>>
>> Jmol.___JmolVersion="14.12.1"
>>
>> bug fix: NBO update
>> bug fix: JavaScript bug - missing  Math.signum(f) - causes
>> {atom}.chirality to not work in JSmol
>>
>> JmolVersion="14.12.0" // 2017-04-06
>>
>> new feature: {atom}.chirality
>>   -- also SELECT chirality = 'R'# or SELECT chirality != ""
>>   -- uses Cahn-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
>>
>>
>>
>> --
>> 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
>>
>>
>>
>> 
>> --
>> 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 list
>> Jmol-users@lists.sourceforge.net
>> 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
>
>
>
>
> 
> --
> 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 list
> Jmol-users@lists.sourceforge.net
> 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
--
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 list
Jmol-users@lists.sourceforge.net
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