Re: [Jmol-users] Jmol 14.14.1 chirality

[Robert Hanson]

argh.  Broke chirality for ketones!

On Fri, Apr 21, 2017 at 11:27 AM, Robert Hanson  wrote:

>
>
> On Fri, Apr 21, 2017 at 11:10 AM, Bruce Tattershall <
> bruce.tattersh...@newcastle.ac.uk> wrote:
>
>> Dear Bob
>>
>>
>>
>> The chirality calculation is clearly useful.
>>
>>
>>
>> I have tried it on my chiral phosphorus compounds, e.g. as in
>>
>> https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php
>>
>> and it finds the chiral carbons in the organic ligands and successfully
>> labels them (as R in this case),
>>
>> but it does not find the chirality of the phosphorus atoms to which they
>> are attached.
>>
>>
> It's a work in progress.
>
> Limitations:
>
>  no parallel chirality paths
>  not processing inositols correctly
>  no lone-pair business
>  standard E/Z, R/S, r/s only; no allenes, no planar asymmetry
>
>
>
>>
>> I have no idea of how this works, but would it be possible to extend it
>> easily to phosphorus chirality (for which
>>
>> one uses the same rules but counts the lone pair as lowest priority)?
>>
>>
> Lone pairs wouldn't be too difficult to add, particularly if they are
> limited to P and S. They are definitely in the IUPAC 2013 spec. I'd like to
> add imine stereochemistry as well.
>
>
>
>>
>>
>> When I first got into measuring NMR spectra of diastereomers of such
>> compounds about 15 years ago,
>>
>> I found it very hard to get my inorganic chemist’s head around the
>> chirality implications.  It would
>>
>> have been very useful to have a tool to work it out for me.
>>
>>
>>
>> If you are going to elements other than carbon, then I guess that besides
>> phosphorus, the inorganic
>>
>> chemist’s favourite, the chirality at silicon, germanium and arsenic
>> could also be useful to people.
>>
>
> Silicon and ammonium are just like carbon, I think. As and P no problem.
>
> Definitely not going to higher valencies any time soon.
>
> Higher priorities are allenes and getting the darned inositol business
> working  correctly. But maybe P and S and As are so easy I should just do
> them
>
> Bob
>



-- 
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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Re: [Jmol-users] Jmol 14.14.1 contour isosurfaces as .pmesh files

[Bruce Tattershall]

Dear Bob

I have been trying out your new .pmesh feature.  It works well for me, both in 
JSmol and in Jmol_S.

Thanks very much:   that solves my timing problems with orbital contour plots 
in a plane, and  I will work
on converting the web pages concerned to read in pre-saved isosurfaces instead 
of calculating them
from the orbital data.   I will read contours from .pmesh files and orbital 
surfaces from .jvxl files.

The only thing I noticed was that the .pmesh files were rather large at half a 
megabyte each, for pretty small
orbitals with only 21 contours, extending over about 5 Angstroms each.  I found 
that these could be
compressed using gzip to about 140 kB, and Jmol_S or JSmol would still read 
them without obviously more
delay.

I just wonder whether all that precision is necessary, for models which are 
only going to be assessed by eye,
relatively quickly.I don’t know how easy it is to control numeric output 
format in the languages you are
using, or whether lower precision would be compatible with existing routines 
for reading .pmesh files.

It just occurred to me that if one was going to use this method a lot, it would 
save server file space
and users’ downloads if the files could be a bit smaller.

Thanks again

Bruce

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 20 April 2017 16:47
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol 14.14.1

OK - this is better:  Looking for the latest version? Download 
Jmol-14.14.1-binary.zip (69.7 MB) 
<https://sourceforge.net/projects/jmol/files/latest/download?source=files>

On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson 
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
hmm. something is missing there. I had to delete that and will upload again.

On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson 
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
Jmol.___JmolVersion="14.14.1" // released 4/19/17


new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
  -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file format)
  -- relatively compact format
  -- can speed up loading of meshes and contours
  -- for filled surfaces, use .jvxl instead
  -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
  -- note that binary files are NOT RECOMMENDED for JSmol because some 
platforms cannot read them locally
  -- example:

  load $methane
  isosurface plane {0 0 0 1} map vdw contours 20
  write ISOSURFACE contour.pmb
  isosurface contour.pmb


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Re: [Jmol-users] Jmol 14.14.1 chirality

[Robert Hanson]

On Fri, Apr 21, 2017 at 11:10 AM, Bruce Tattershall <
bruce.tattersh...@newcastle.ac.uk> wrote:

> Dear Bob
>
>
>
> The chirality calculation is clearly useful.
>
>
>
> I have tried it on my chiral phosphorus compounds, e.g. as in
>
> https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php
>
> and it finds the chiral carbons in the organic ligands and successfully
> labels them (as R in this case),
>
> but it does not find the chirality of the phosphorus atoms to which they
> are attached.
>
>
It's a work in progress.

Limitations:

 no parallel chirality paths
 not processing inositols correctly
 no lone-pair business
 standard E/Z, R/S, r/s only; no allenes, no planar asymmetry



>
> I have no idea of how this works, but would it be possible to extend it
> easily to phosphorus chirality (for which
>
> one uses the same rules but counts the lone pair as lowest priority)?
>
>
Lone pairs wouldn't be too difficult to add, particularly if they are
limited to P and S. They are definitely in the IUPAC 2013 spec. I'd like to
add imine stereochemistry as well.



>
>
> When I first got into measuring NMR spectra of diastereomers of such
> compounds about 15 years ago,
>
> I found it very hard to get my inorganic chemist’s head around the
> chirality implications.  It would
>
> have been very useful to have a tool to work it out for me.
>
>
>
> If you are going to elements other than carbon, then I guess that besides
> phosphorus, the inorganic
>
> chemist’s favourite, the chirality at silicon, germanium and arsenic could
> also be useful to people.
>

Silicon and ammonium are just like carbon, I think. As and P no problem.

Definitely not going to higher valencies any time soon.

Higher priorities are allenes and getting the darned inositol business
working  correctly. But maybe P and S and As are so easy I should just do
them

Bob
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Re: [Jmol-users] Jmol 14.14.1 chirality

[Bruce Tattershall]

Dear Bob

The chirality calculation is clearly useful.

I have tried it on my chiral phosphorus compounds, e.g. as in
https://www.staff.ncl.ac.uk/bruce.tattershall/structs/bpthiq.php
and it finds the chiral carbons in the organic ligands and successfully labels 
them (as R in this case),
but it does not find the chirality of the phosphorus atoms to which they are 
attached.

I have no idea of how this works, but would it be possible to extend it easily 
to phosphorus chirality (for which
one uses the same rules but counts the lone pair as lowest priority)?

When I first got into measuring NMR spectra of diastereomers of such compounds 
about 15 years ago,
I found it very hard to get my inorganic chemist’s head around the chirality 
implications.  It would
have been very useful to have a tool to work it out for me.

If you are going to elements other than carbon, then I guess that besides 
phosphorus, the inorganic
chemist’s favourite, the chirality at silicon, germanium and arsenic could also 
be useful to people.

Best wishes

   Bruce

Bruce Tattershall
School of Chemistry
Newcastle University
England

From: Robert Hanson [mailto:hans...@stolaf.edu]
Sent: 20 April 2017 16:47
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Jmol 14.14.1

OK - this is better:  Looking for the latest version? Download 
Jmol-14.14.1-binary.zip (69.7 MB) 
<https://sourceforge.net/projects/jmol/files/latest/download?source=files>

On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson 
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
hmm. something is missing there. I had to delete that and will upload again.

On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson 
<hans...@stolaf.edu<mailto:hans...@stolaf.edu>> wrote:
Jmol.___JmolVersion="14.14.1" // released 4/19/17

new feature: CALCULATE CHIRALITY {atom set}
  -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
  -- continues with Rules 3-5, which require full-molecule analysis.
  -- work in progress:
 -- Rules 1 and 2 complete
 -- Rule 3 (E/Z) implemented
 -- Rule 4 partially implemented
-- simple linear sequences of R/S ok
 -- Rule 5 not implemented
  -- caveates
 -- no pseudochirality
 -- not cyclitols
 -- does not distinguish rings, so inserts "Z" into ring bonds
 -- only validated on

  -- optionally limited to the given atom set (or the currently selected atoms 
by default)


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Re: [Jmol-users] Jmol 14.14.1

[Pshemak Maslak]

I can confirm: the command (in bold below) generated the expected closed 
CAP surfaces in Jmol and JSmol.


Thanks Bob,

PM


On 4/20/2017 10:34 PM, Robert Hanson wrote:



On Thu, Apr 20, 2017 at 8:35 AM, Pshemak Maslak > wrote:


Bob;

I am looking forward to exploring the new R/S and E/Z
functionality; it's a great addition.

Does this version include fix for "/*spacefill ionic;lcaocartoon
scale 1.0 CAP unitcell "cpk";spacefill off" */which freezes the
Jmol (Java) and leaves open surfaces (no "cap') on many unticell
faces in JSmol?


yes, I think so. Please test. Also the fact that sometimes caps were 
not completely closed.


Thanks,

PM




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Re: [Jmol-users] Jmol 14.14.1

[Robert Hanson]

On Thu, Apr 20, 2017 at 8:35 AM, Pshemak Maslak  wrote:

> Bob;
>
> I am looking forward to exploring the new R/S and E/Z functionality; it's
> a great addition.
>
> Does this version include fix for "*spacefill ionic;lcaocartoon scale 1.0
> CAP unitcell "cpk";spacefill off" *which freezes the Jmol (Java) and
> leaves open surfaces (no "cap') on many unticell faces in JSmol?
>
>
yes, I think so. Please test. Also the fact that sometimes caps were not
completely closed.


> Thanks,
>
> PM
>
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Re: [Jmol-users] Jmol 14.14.1

[Arturo Manzo-Fontes]

Thanks Robert, it works fine!

Best.

Arturo Manzo-Fontes, Ph.D.
COO
*Spleißen Wege Bio, S. de R.L. de C.V.*



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Este mensaje, incluyendo sus anexos, contiene información confidencial y se
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 Gracias.

2017-04-20 10:47 GMT-05:00 Robert Hanson :

> OK - this is better:  Looking for the latest version? * Download
> Jmol-14.14.1-binary.zip (69.7 MB)
>  *
>
> On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson 
> wrote:
>
>> hmm. something is missing there. I had to delete that and will upload
>> again.
>>
>> On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson 
>> wrote:
>>
>>> Jmol.___JmolVersion="14.14.1" // released 4/19/17
>>>
>>> new feature: CALCULATE CHIRALITY {atom set}
>>>   -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
>>>   -- continues with Rules 3-5, which require full-molecule analysis.
>>>   -- work in progress:
>>>  -- Rules 1 and 2 complete
>>>  -- Rule 3 (E/Z) implemented
>>>  -- Rule 4 partially implemented
>>> -- simple linear sequences of R/S ok
>>>  -- Rule 5 not implemented
>>>   -- caveates
>>>  -- no pseudochirality
>>>  -- not cyclitols
>>>  -- does not distinguish rings, so inserts "Z" into ring bonds
>>>  -- only validated on
>>>
>>>   -- optionally limited to the given atom set (or the currently selected
>>> atoms by default)
>>>
>>> new feature: set jmolInJSpecView
>>>   -- allows Jmol window to NOT be embedded in JSpecView when JSpecView
>>> is opened in Jmol
>>>   -- default TRUE
>>>
>>> new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
>>>   -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
>>> format)
>>>   -- relatively compact format
>>>   -- can speed up loading of meshes and contours
>>>   -- for filled surfaces, use .jvxl instead
>>>   -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
>>>   -- note that binary files are NOT RECOMMENDED for JSmol because some
>>> platforms cannot read them locally
>>>   -- example:
>>>
>>>   load $methane
>>>   isosurface plane {0 0 0 1} map vdw contours 20
>>>   write ISOSURFACE contour.pmb
>>>   isosurface contour.pmb
>>>
>>>
>>> bug fix: mesh capper producing gaps
>>> bug fix: CIP chirality fixed for rule ordering; validated for IUPAC
>>> Rules 1, 2, and 3 (though still some questions about Rule 3)
>>> bug fix: print getProperty("cifinfo") without file name fails
>>>
>>>
>>>
>>>
>>> --
>>> 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
>
>
> 
> --
> Check out the vibrant tech community on one 

Re: [Jmol-users] Jmol 14.14.1

[Pshemak Maslak]

Bob;

I am looking forward to exploring the new R/S and E/Z functionality; 
it's a great addition!


Does this version include fix for "/*spacefill ionic;lcaocartoon scale 
1.0 CAP unitcell "cpk";spacefill off" */which freezes the Jmol (Java) 
and leaves open surfaces (no "cap') on many unticell faces in JSmol?


Thanks,

PM


On 4/20/2017 11:47 AM, Robert Hanson wrote:
OK - this is better:  Looking for the latest version? *Download 
Jmol-14.14.1-binary.zip (69.7 MB) 
 
*


On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson > wrote:


hmm. something is missing there. I had to delete that and will
upload again.

On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson
> wrote:

Jmol.___JmolVersion="14.14.1" // released 4/19/17

new feature: CALCULATE CHIRALITY {atom set}
  -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
  -- continues with Rules 3-5, which require full-molecule
analysis.
  -- work in progress:
 -- Rules 1 and 2 complete
 -- Rule 3 (E/Z) implemented
 -- Rule 4 partially implemented
-- simple linear sequences of R/S ok
 -- Rule 5 not implemented
  -- caveates
 -- no pseudochirality
 -- not cyclitols
 -- does not distinguish rings, so inserts "Z" into ring bonds
 -- only validated on

  -- optionally limited to the given atom set (or the
currently selected atoms by default)

new feature: set jmolInJSpecView
  -- allows Jmol window to NOT be embedded in JSpecView when
JSpecView is opened in Jmol
  -- default TRUE

new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
  -- creates ASCII (.pmesh) or binary (.pmb) file (a
Jmol-specific file format)
  -- relatively compact format
  -- can speed up loading of meshes and contours
  -- for filled surfaces, use .jvxl instead
  -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
  -- note that binary files are NOT RECOMMENDED for JSmol
because some platforms cannot read them locally
  -- example:

  load $methane
  isosurface plane {0 0 0 1} map vdw contours 20
  write ISOSURFACE contour.pmb
  isosurface contour.pmb


bug fix: mesh capper producing gaps
bug fix: CIP chirality fixed for rule ordering; validated for
IUPAC Rules 1, 2, and 3 (though still some questions about Rule 3)
bug fix: print getProperty("cifinfo") without file name fails




-- 
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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Re: [Jmol-users] Jmol 14.14.1

[Robert Hanson]

OK - this is better:  Looking for the latest version? * Download
Jmol-14.14.1-binary.zip (69.7 MB)
 *

On Wed, Apr 19, 2017 at 11:35 PM, Robert Hanson  wrote:

> hmm. something is missing there. I had to delete that and will upload
> again.
>
> On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson 
> wrote:
>
>> Jmol.___JmolVersion="14.14.1" // released 4/19/17
>>
>> new feature: CALCULATE CHIRALITY {atom set}
>>   -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
>>   -- continues with Rules 3-5, which require full-molecule analysis.
>>   -- work in progress:
>>  -- Rules 1 and 2 complete
>>  -- Rule 3 (E/Z) implemented
>>  -- Rule 4 partially implemented
>> -- simple linear sequences of R/S ok
>>  -- Rule 5 not implemented
>>   -- caveates
>>  -- no pseudochirality
>>  -- not cyclitols
>>  -- does not distinguish rings, so inserts "Z" into ring bonds
>>  -- only validated on
>>
>>   -- optionally limited to the given atom set (or the currently selected
>> atoms by default)
>>
>> new feature: set jmolInJSpecView
>>   -- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
>> opened in Jmol
>>   -- default TRUE
>>
>> new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
>>   -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
>> format)
>>   -- relatively compact format
>>   -- can speed up loading of meshes and contours
>>   -- for filled surfaces, use .jvxl instead
>>   -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
>>   -- note that binary files are NOT RECOMMENDED for JSmol because some
>> platforms cannot read them locally
>>   -- example:
>>
>>   load $methane
>>   isosurface plane {0 0 0 1} map vdw contours 20
>>   write ISOSURFACE contour.pmb
>>   isosurface contour.pmb
>>
>>
>> bug fix: mesh capper producing gaps
>> bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules
>> 1, 2, and 3 (though still some questions about Rule 3)
>> bug fix: print getProperty("cifinfo") without file name fails
>>
>>
>>
>>
>> --
>> 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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Re: [Jmol-users] Jmol 14.14.1

[Pshemak Maslak]

Bob;

I am looking forward to exploring the new R/S and E/Z functionality; 
it's a great addition.


Does this version include fix for "/*spacefill ionic;lcaocartoon scale 
1.0 CAP unitcell "cpk";spacefill off" */which freezes the Jmol (Java) 
and leaves open surfaces (no "cap') on many unticell faces in JSmol?


Thanks,

PM



On 4/20/2017 12:29 AM, Robert Hanson wrote:
link for this release: *Download Jmol-14.14.1-binary.zip (65.0 MB) 
 
*







bug fix: mesh capper producing gaps
bug fix: CIP chirality fixed for rule ordering; validated for
IUPAC Rules 1, 2, and 3 (though still some questions about Rule 3)
bug fix: print getProperty("cifinfo") without file name fails





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Re: [Jmol-users] Jmol 14.14.1

[Pierluigi Quagliotto]

Many thanks, Bob!

Wonderful news! I am waiting for the availability of the release to 
imrpove my page on chirality and to prepare also a page to introduce all 
the steps needed to assign E/Z configurations.


Bye!

Pierluigi

Il 20/04/2017 06:28, Robert Hanson ha scritto:

Jmol.___JmolVersion="14.14.1" // released 4/19/17

new feature: CALCULATE CHIRALITY {atom set}
  -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
  -- continues with Rules 3-5, which require full-molecule analysis.
  -- work in progress:
 -- Rules 1 and 2 complete
 -- Rule 3 (E/Z) implemented
 -- Rule 4 partially implemented
-- simple linear sequences of R/S ok
 -- Rule 5 not implemented
  -- caveates
 -- no pseudochirality
 -- not cyclitols
 -- does not distinguish rings, so inserts "Z" into ring bonds
 -- only validated on

  -- optionally limited to the given atom set (or the currently 
selected atoms by default)


new feature: set jmolInJSpecView
  -- allows Jmol window to NOT be embedded in JSpecView when JSpecView 
is opened in Jmol

  -- default TRUE

new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
  -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific 
file format)

  -- relatively compact format
  -- can speed up loading of meshes and contours
  -- for filled surfaces, use .jvxl instead
  -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
  -- note that binary files are NOT RECOMMENDED for JSmol because some 
platforms cannot read them locally

  -- example:

  load $methane
  isosurface plane {0 0 0 1} map vdw contours 20
  write ISOSURFACE contour.pmb
  isosurface contour.pmb


bug fix: mesh capper producing gaps
bug fix: CIP chirality fixed for rule ordering; validated for IUPAC 
Rules 1, 2, and 3 (though still some questions about Rule 3)

bug fix: print getProperty("cifinfo") without file name fails




--
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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Re: [Jmol-users] Jmol 14.14.1

[Robert Hanson]

hmm. something is missing there. I had to delete that and will upload again.

On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson  wrote:

> Jmol.___JmolVersion="14.14.1" // released 4/19/17
>
> new feature: CALCULATE CHIRALITY {atom set}
>   -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
>   -- continues with Rules 3-5, which require full-molecule analysis.
>   -- work in progress:
>  -- Rules 1 and 2 complete
>  -- Rule 3 (E/Z) implemented
>  -- Rule 4 partially implemented
> -- simple linear sequences of R/S ok
>  -- Rule 5 not implemented
>   -- caveates
>  -- no pseudochirality
>  -- not cyclitols
>  -- does not distinguish rings, so inserts "Z" into ring bonds
>  -- only validated on
>
>   -- optionally limited to the given atom set (or the currently selected
> atoms by default)
>
> new feature: set jmolInJSpecView
>   -- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
> opened in Jmol
>   -- default TRUE
>
> new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
>   -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
> format)
>   -- relatively compact format
>   -- can speed up loading of meshes and contours
>   -- for filled surfaces, use .jvxl instead
>   -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
>   -- note that binary files are NOT RECOMMENDED for JSmol because some
> platforms cannot read them locally
>   -- example:
>
>   load $methane
>   isosurface plane {0 0 0 1} map vdw contours 20
>   write ISOSURFACE contour.pmb
>   isosurface contour.pmb
>
>
> bug fix: mesh capper producing gaps
> bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules
> 1, 2, and 3 (though still some questions about Rule 3)
> bug fix: print getProperty("cifinfo") without file name fails
>
>
>
>
> --
> 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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Re: [Jmol-users] Jmol 14.14.1

[Robert Hanson]

link for this release: * Download Jmol-14.14.1-binary.zip (65.0 MB)
 *

On Wed, Apr 19, 2017 at 11:28 PM, Robert Hanson  wrote:

> Jmol.___JmolVersion="14.14.1" // released 4/19/17
>
> new feature: CALCULATE CHIRALITY {atom set}
>   -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
>   -- continues with Rules 3-5, which require full-molecule analysis.
>   -- work in progress:
>  -- Rules 1 and 2 complete
>  -- Rule 3 (E/Z) implemented
>  -- Rule 4 partially implemented
> -- simple linear sequences of R/S ok
>  -- Rule 5 not implemented
>   -- caveates
>  -- no pseudochirality
>  -- not cyclitols
>  -- does not distinguish rings, so inserts "Z" into ring bonds
>  -- only validated on
>
>   -- optionally limited to the given atom set (or the currently selected
> atoms by default)
>
> new feature: set jmolInJSpecView
>   -- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
> opened in Jmol
>   -- default TRUE
>
> new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
>   -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
> format)
>   -- relatively compact format
>   -- can speed up loading of meshes and contours
>   -- for filled surfaces, use .jvxl instead
>   -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
>   -- note that binary files are NOT RECOMMENDED for JSmol because some
> platforms cannot read them locally
>   -- example:
>
>   load $methane
>   isosurface plane {0 0 0 1} map vdw contours 20
>   write ISOSURFACE contour.pmb
>   isosurface contour.pmb
>
>
> bug fix: mesh capper producing gaps
> bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules
> 1, 2, and 3 (though still some questions about Rule 3)
> bug fix: print getProperty("cifinfo") without file name fails
>
>
>
>
> --
> 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
--
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 14.14.1

[Robert Hanson]

Jmol.___JmolVersion="14.14.1" // released 4/19/17

new feature: CALCULATE CHIRALITY {atom set}
  -- starts with basic CIP Rule 1-2 determination of R/S and E/Z.
  -- continues with Rules 3-5, which require full-molecule analysis.
  -- work in progress:
 -- Rules 1 and 2 complete
 -- Rule 3 (E/Z) implemented
 -- Rule 4 partially implemented
-- simple linear sequences of R/S ok
 -- Rule 5 not implemented
  -- caveates
 -- no pseudochirality
 -- not cyclitols
 -- does not distinguish rings, so inserts "Z" into ring bonds
 -- only validated on

  -- optionally limited to the given atom set (or the currently selected
atoms by default)

new feature: set jmolInJSpecView
  -- allows Jmol window to NOT be embedded in JSpecView when JSpecView is
opened in Jmol
  -- default TRUE

new feature: WRITE ISOSURFACE "t.pmesh"; WRITE ISOSURFACE "t.pmb"
  -- creates ASCII (.pmesh) or binary (.pmb) file (a Jmol-specific file
format)
  -- relatively compact format
  -- can speed up loading of meshes and contours
  -- for filled surfaces, use .jvxl instead
  -- read back into Jmol using ISOSURFACE "t.pmesh"/"t.pmb"
  -- note that binary files are NOT RECOMMENDED for JSmol because some
platforms cannot read them locally
  -- example:

  load $methane
  isosurface plane {0 0 0 1} map vdw contours 20
  write ISOSURFACE contour.pmb
  isosurface contour.pmb


bug fix: mesh capper producing gaps
bug fix: CIP chirality fixed for rule ordering; validated for IUPAC Rules
1, 2, and 3 (though still some questions about Rule 3)
bug fix: print getProperty("cifinfo") without file name fails




-- 
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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