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

2017-04-09 Thread Robert Hanson 
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%
> 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 
> 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___
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Re: [Jmol-users] Jmol 14.12.1 released -- R/S chirality

2017-04-09 Thread Pierluigi Quagliotto 

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


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[Jmol-users] Jmol 14.13.1

2017-04-09 Thread Robert Hanson 
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.13/Jmol%2014.13.1/

Jmol.___JmolVersion="14.13.1" // 2017.04.09

new feature: set labelfor {atomset} "value"
 -- allows setting of label without changing current selection
 -- uses same syntax as LABEL command after {atomset}
 -- for example:

   set labelfor @atoms @myLabel
   set labelfor {atomno <= 3} @{["a","b","c"]}
   set labelfor {_C && chirality != ""} "%[atomname] %[chirality]"

new feature: MOL V2000 reader loads >  blocks into _M.molData

bug fix: {*}.chirality with triple bonds fails
bug fix: {*}.chirality fix for duplicated atoms check

bug fix: dotted line has annoying extra dot: measure ID m @1 @4 radius 0.1

bug fix: NBO H-BOND and MODEL focus issues



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

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

2017-04-09 Thread pinostricc...@alice.it 
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
  

  
  

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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 list
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