Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Otis Rothenberger 
Dean and Pshemak,

First, OK I'm a believer. The command "display unitcell" is real, and it's 
neat. It cuts off all of the exterior atoms (to unit cell). That's good to know.

On the desktop app issue, I think I was one of the early users to say good-bye 
to Java. I'm a small molecule guy, and Bob saved me with JSmol. As a small 
molecule guy, I can get away with my no-Java approach. 

Unfortunately, I can't be of much help with Java app questions.

On your final question, can you send me (point me to) the CIF file? I'm 
assuming from the context of this question that this is the JSmol version. Is 
that correct?

Otis

--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org

> On Apr 10, 2017, at 1:21 PM, Pshemak Maslak  wrote:
> 
> Otis and Dean,,
> 
> Thanks for the explanation. I was indeed able to find the whole command 
> (spacefill ionic;lcaocartoon scale 1.0 CAP unitcell "cpk";spacefill off)  in 
> the documentation (in the "cpk" example of lcaoCartoons).
> 
> I think I understand it better now. The "spacefill" spheres are replaced with 
> "cpk" spheres" which then are SLAB-ed (CAP-ed really) using "unitcell" as 
> slabbing planes. 
> 
> I tried it on NaCl (cif file). It works on a cell containing one Cl-  in the 
> center of the cell and one Na+  in the corner (which is properly CAP-ed). 
> 
> However when I load {1 1 1} cell to get all ions within the cell, the Jmol 
> (desktop Java app) freezes. I tried the newest version (14.13.1) an an older 
> one (14.8.0) with the same results.
> 
> I tried  Na (cif)  (loading {2 2 2} and using "display unitcell" (which show 
> all needed atoms), but "lcaocartoon scale 1.0 CAP unitcell "cpk";spacefill 
> off"  froze Jmol as well.
> 
> Any suggestions?
> 
> Thanks for your help.
> 
> PM 
> 
> 
> 
> On 4/10/2017 12:08 PM, Otis Rothenberger wrote:
>> Pshemak,
>> 
>> The CAP part is discussed here:
>> 
>> https://chemapps.stolaf.edu/jmol/docs/index.htm?=1=14.6#isosurface
>>  
>> 
>> 
>> Scroll down until you see CAP listing.
>> 
>> The spacefill 1% is just hiding the atoms leaving the lcaocartoons
>> 
>> Dean, the main reason I'm jumping in here is the display unitcell command. 
>> Is that a legal Jmol Script command? After loading a CIF file, I thought 
>> that you had to do something like this to get the unit cell:
>> 
>> save orientation; load "" {444 666 1}; set displayCellParameters 
>> false;restore orientation; unitcell on; display cell=555; center visible; 
>> zoom 200;
>> 
>> Otis
>> 
>> --
>> Otis Rothenberger
>> o...@chemagic.org 
>> http://chemagic.org 
>>> On Apr 10, 2017, at 11:44 AM, Pshemak Maslak >> > wrote:
>>> 
>>> Thank you Dean, 
>>> 
>>> I do not understand the
>>> 
>>> lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%; 
>>> 
>>> part of the command. Is it documented in 
>>> https://chemapps.stolaf.edu/jmol/docs/ 
>>>   ?
>>> 
>>> Thanks,
>>> 
>>> PM
>>> 
>>> 
>>> On 4/10/2017 10:46 AM, Dean Johnston wrote:
 Yes - I have an example at: 
 http://crystals.otterbein.edu/packing/index.html 
 
 
 Pick structure from the left menu and then click the “Show Contents of One 
 Unit Cell”. Works beautifully!
 
 The commands are:
 display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP unitcell 
 'cpk'; spacefill 1%; 
 
 Dean Johnston
 
 On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu 
 ) wrote:
 
> 
> Can the "slab" command be used to produce presentations equivalent to the 
> image linked below?
> 
> https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg
>  
> 
> 
> If so, any suggestions on how to do that would be appreciated.
> 
> Thanks,
> 
> PM
> --
>  
> 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 
>  
 
 
 --
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Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Pshemak Maslak 

Thank you Dean,

I do not understand the

   lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%; 



part of the command. Is it documented in 
https://chemapps.stolaf.edu/jmol/docs/  ?


Thanks,

PM


On 4/10/2017 10:46 AM, Dean Johnston wrote:
Yes - I have an example at: 
http://crystals.otterbein.edu/packing/index.html


Pick structure from the left menu and then click the “Show Contents of 
One Unit Cell”. Works beautifully!


The commands are:
display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP 
unitcell 'cpk'; spacefill 1%;


Dean Johnston

On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu 
) wrote:




Can the "slab" command be used to produce presentations equivalent to 
the image linked below?


https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg

If so, any suggestions on how to do that would be appreciated.

Thanks,

PM
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Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Pshemak Maslak 

Thank you Dean,

I do not understand the

   lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%; 



part of the command. Is it documented in 
https://chemapps.stolaf.edu/jmol/docs/  ?


Thanks,

PM


On 4/10/2017 10:46 AM, Dean Johnston wrote:
Yes - I have an example at: 
http://crystals.otterbein.edu/packing/index.html


Pick structure from the left menu and then click the “Show Contents of 
One Unit Cell”. Works beautifully!


The commands are:
display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP 
unitcell 'cpk'; spacefill 1%;


Dean Johnston

On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu 
) wrote:




Can the "slab" command be used to produce presentations equivalent to 
the image linked below?


https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg

If so, any suggestions on how to do that would be appreciated.

Thanks,

PM
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Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Otis Rothenberger 
Pshemak,

The CAP part is discussed here:

https://chemapps.stolaf.edu/jmol/docs/index.htm?=1=14.6#isosurface
 


Scroll down until you see CAP listing.

The spacefill 1% is just hiding the atoms leaving the lcaocartoons

Dean, the main reason I'm jumping in here is the display unitcell command. Is 
that a legal Jmol Script command? After loading a CIF file, I thought that you 
had to do something like this to get the unit cell:

save orientation; load "" {444 666 1}; set displayCellParameters false;restore 
orientation; unitcell on; display cell=555; center visible; zoom 200;

Otis

--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org

> On Apr 10, 2017, at 11:44 AM, Pshemak Maslak  wrote:
> 
> Thank you Dean, 
> 
> I do not understand the
> 
> lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%; 
> 
> part of the command. Is it documented in 
> https://chemapps.stolaf.edu/jmol/docs/ 
>   ?
> 
> Thanks,
> 
> PM
> 
> 
> On 4/10/2017 10:46 AM, Dean Johnston wrote:
>> Yes - I have an example at: http://crystals.otterbein.edu/packing/index.html 
>> 
>> 
>> Pick structure from the left menu and then click the “Show Contents of One 
>> Unit Cell”. Works beautifully!
>> 
>> The commands are:
>> display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP unitcell 
>> 'cpk'; spacefill 1%; 
>> 
>> Dean Johnston
>> 
>> On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu 
>> ) wrote:
>> 
>>> 
>>> Can the "slab" command be used to produce presentations equivalent to the 
>>> image linked below?
>>> 
>>> https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg
>>>  
>>> 
>>> 
>>> If so, any suggestions on how to do that would be appreciated.
>>> 
>>> Thanks,
>>> 
>>> PM
>>> --
>>>  
>>> 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 
>>>  
>> 
>> 
>> --
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>> engaging tech sites, Slashdot.org ! 
>> http://sdm.link/slashdot 
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>> 
> 
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Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Pshemak Maslak 

Otis and Dean,,

Thanks for the explanation. I was indeed able to find the whole command 
(spacefill ionic;lcaocartoon scale 1.0 CAP unitcell "cpk";spacefill 
off/) / in the documentation (in the "cpk" example of lcaoCartoons).


I think I understand it better now. The "spacefill" spheres are replaced 
with "cpk" spheres" which then are SLAB-ed (CAP-ed really) using 
"unitcell" as slabbing planes.


I tried it on NaCl (cif file). It works on a cell containing one Cl-  in 
the center of the cell and one Na+  in the corner (which is properly 
CAP-ed).


However when I load {1 1 1} cell to get all ions within the cell, the 
Jmol (desktop Java app) freezes. I tried the newest version (14.13.1) an 
an older one (14.8.0) with the same results.


I tried  Na (cif)  (loading {2 2 2} and using "display unitcell" (which 
show all needed atoms), but "lcaocartoon scale 1.0 CAP unitcell 
"cpk";spacefill off"  froze Jmol as well.


Any suggestions?

Thanks for your help.

PM



On 4/10/2017 12:08 PM, Otis Rothenberger wrote:

Pshemak,

The CAP part is discussed here:

https://chemapps.stolaf.edu/jmol/docs/index.htm?=1=14.6#isosurface

Scroll down until you see CAP listing.

The spacefill 1% is just hiding the atoms leaving the lcaocartoons

Dean, the main reason I'm jumping in here is the display unitcell 
command. Is that a legal Jmol Script command? After loading a CIF 
file, I thought that you had to do something like this to get the unit 
cell:


save orientation; load "" {444 666 1}; set displayCellParameters 
false;restore orientation; unitcell on; display cell=555; center 
visible; zoom 200;


Otis

--
Otis Rothenberger
o...@chemagic.org 
http://chemagic.org

On Apr 10, 2017, at 11:44 AM, Pshemak Maslak > wrote:


Thank you Dean,

I do not understand the

lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%; 



part of the command. Is it documented 
inhttps://chemapps.stolaf.edu/jmol/docs/ ?


Thanks,

PM


On 4/10/2017 10:46 AM, Dean Johnston wrote:
Yes - I have an example at: 
http://crystals.otterbein.edu/packing/index.html


Pick structure from the left menu and then click the “Show Contents 
of One Unit Cell”. Works beautifully!


The commands are:
display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP 
unitcell 'cpk'; spacefill 1%;


Dean Johnston

On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu 
) wrote:




Can the "slab" command be used to produce presentations equivalent 
to the image linked below?


https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg

If so, any suggestions on how to do that would be appreciated.

Thanks,

PM
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Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Dean Johnston 
Pshemak, Otis and Bob,

Glad that I could provide something to the list. I have to admit that I set
that page up long enough ago that I can't recall exactly how I figured it
out. But it still works and it's useful.

Dean

On Mon, Apr 10, 2017 at 3:09 PM, Robert Hanson  wrote:

> OK, I know how I my comparison method violated the general contract. Very
> surprised this ever worked!
>
> On Mon, Apr 10, 2017 at 1:37 PM, Robert Hanson  wrote:
>
>> Pshemak,
>>
>> Gotta love this error message:
>>
>> java.lang.IllegalArgumentException: Comparison method violates its
>> general contract!
>>
>> I'll check on this.
>>
>> Bob
>>
>>
>> On Mon, Apr 10, 2017 at 12:21 PM, Pshemak Maslak  wrote:
>>
>>> Otis and Dean,,
>>>
>>> Thanks for the explanation. I was indeed able to find the whole command
>>> (spacefill ionic;lcaocartoon scale 1.0 CAP unitcell "cpk";spacefill off
>>> *) * in the documentation (in the "cpk" example of lcaoCartoons).
>>>
>>> I think I understand it better now. The "spacefill" spheres are replaced
>>> with "cpk" spheres" which then are SLAB-ed (CAP-ed really) using "unitcell"
>>> as slabbing planes.
>>>
>>> I tried it on NaCl (cif file). It works on a cell containing one Cl-  in
>>> the center of the cell and one Na+  in the corner (which is properly
>>> CAP-ed).
>>>
>>> However when I load {1 1 1} cell to get all ions within the cell, the
>>> Jmol (desktop Java app) freezes. I tried the newest version (14.13.1) an an
>>> older one (14.8.0) with the same results.
>>>
>>> I tried  Na (cif)  (loading {2 2 2} and using "display unitcell" (which
>>> show all needed atoms), but "lcaocartoon scale 1.0 CAP unitcell
>>> "cpk";spacefill off"  froze Jmol as well.
>>>
>>> Any suggestions?
>>>
>>> Thanks for your help.
>>>
>>> PM
>>>
>>>
>>>
>>> On 4/10/2017 12:08 PM, Otis Rothenberger wrote:
>>>
>>> Pshemak,
>>>
>>> The CAP part is discussed here:
>>>
>>> https://chemapps.stolaf.edu/jmol/docs/index.htm?=
>>> 1=14.6#isosurface
>>>
>>> Scroll down until you see CAP listing.
>>>
>>> The spacefill 1% is just hiding the atoms leaving the lcaocartoons
>>>
>>> Dean, the main reason I'm jumping in here is the display unitcell
>>> command. Is that a legal Jmol Script command? After loading a CIF file, I
>>> thought that you had to do something like this to get the unit cell:
>>>
>>> save orientation; load "" {444 666 1}; set displayCellParameters
>>> false;restore orientation; unitcell on; display cell=555; center visible;
>>> zoom 200;
>>>
>>> Otis
>>>
>>> --
>>> Otis Rothenberger
>>> o...@chemagic.org
>>> http://chemagic.org
>>>
>>> On Apr 10, 2017, at 11:44 AM, Pshemak Maslak  wrote:
>>>
>>> Thank you Dean,
>>>
>>> I do not understand the
>>>
>>> lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%;
>>>
>>>
>>> part of the command. Is it documented in https://chemapps.stolaf.edu
>>> /jmol/docs/  ?
>>>
>>> Thanks,
>>>
>>> PM
>>>
>>>
>>> On 4/10/2017 10:46 AM, Dean Johnston wrote:
>>>
>>> Yes - I have an example at: http://crystals.otterbein.
>>> edu/packing/index.html
>>>
>>> Pick structure from the left menu and then click the “Show Contents of
>>> One Unit Cell”. Works beautifully!
>>>
>>> The commands are:
>>> display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP
>>> unitcell 'cpk'; spacefill 1%;
>>>
>>> Dean Johnston
>>>
>>> On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu) wrote:
>>>
>>>
>>> Can the "slab" command be used to produce presentations equivalent to
>>> the image linked below?
>>>
>>> https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/F
>>> ile:CCC_crystal_cell_(opaque).svg
>>>
>>> If so, any suggestions on how to do that would be appreciated.
>>>
>>> Thanks,
>>>
>>> PM
>>> 
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, Slashdot.org ! http://sd
>>> m.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 
>>> listJmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>> 
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>>> engaging tech sites, Slashdot.org ! http://sd
>>> m.link/slashdot___
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>>>

Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Pshemak Maslak 

Otis and Dean,

I just tested NaCl in JSmol (JavaSript) on a rather old version 
(14.4.1). Surprise: it works as intended (no freezing).


I will do more testing.

Otis, I will send you the cif files to your address (list does not allow 
attachments).


Thanks,

PM

On 4/10/2017 1:49 PM, Otis Rothenberger wrote:

Dean and Pshemak,

First, OK I'm a believer. The command "display unitcell" is real, and 
it's neat. It cuts off all of the exterior atoms (to unit cell). 
That's good to know.


On the desktop app issue, I think I was one of the early users to say 
good-bye to Java. I'm a small molecule guy, and Bob saved me with 
JSmol. As a small molecule guy, I can get away with my no-Java approach.


Unfortunately, I can't be of much help with Java app questions.

On your final question, can you send me (point me to) the CIF file? 
I'm assuming from the context of this question that this is the JSmol 
version. Is that correct?


Otis

--
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o...@chemagic.org 
http://chemagic.org



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Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Robert Hanson 
Pshemak,

Gotta love this error message:

java.lang.IllegalArgumentException: Comparison method violates its general
contract!

I'll check on this.

Bob


On Mon, Apr 10, 2017 at 12:21 PM, Pshemak Maslak  wrote:

> Otis and Dean,,
>
> Thanks for the explanation. I was indeed able to find the whole command
> (spacefill ionic;lcaocartoon scale 1.0 CAP unitcell "cpk";spacefill off
> *) * in the documentation (in the "cpk" example of lcaoCartoons).
>
> I think I understand it better now. The "spacefill" spheres are replaced
> with "cpk" spheres" which then are SLAB-ed (CAP-ed really) using "unitcell"
> as slabbing planes.
>
> I tried it on NaCl (cif file). It works on a cell containing one Cl-  in
> the center of the cell and one Na+  in the corner (which is properly
> CAP-ed).
>
> However when I load {1 1 1} cell to get all ions within the cell, the Jmol
> (desktop Java app) freezes. I tried the newest version (14.13.1) an an
> older one (14.8.0) with the same results.
>
> I tried  Na (cif)  (loading {2 2 2} and using "display unitcell" (which
> show all needed atoms), but "lcaocartoon scale 1.0 CAP unitcell
> "cpk";spacefill off"  froze Jmol as well.
>
> Any suggestions?
>
> Thanks for your help.
>
> PM
>
>
>
> On 4/10/2017 12:08 PM, Otis Rothenberger wrote:
>
> Pshemak,
>
> The CAP part is discussed here:
>
> https://chemapps.stolaf.edu/jmol/docs/index.htm?=1=14.6#
> isosurface
>
> Scroll down until you see CAP listing.
>
> The spacefill 1% is just hiding the atoms leaving the lcaocartoons
>
> Dean, the main reason I'm jumping in here is the display unitcell command.
> Is that a legal Jmol Script command? After loading a CIF file, I thought
> that you had to do something like this to get the unit cell:
>
> save orientation; load "" {444 666 1}; set displayCellParameters
> false;restore orientation; unitcell on; display cell=555; center visible;
> zoom 200;
>
> Otis
>
> --
> Otis Rothenberger
> o...@chemagic.org
> http://chemagic.org
>
> On Apr 10, 2017, at 11:44 AM, Pshemak Maslak  wrote:
>
> Thank you Dean,
>
> I do not understand the
>
> lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%;
>
>
> part of the command. Is it documented in https://chemapps.stolaf.
> edu/jmol/docs/  ?
>
> Thanks,
>
> PM
>
>
> On 4/10/2017 10:46 AM, Dean Johnston wrote:
>
> Yes - I have an example at: http://crystals.otterbein.
> edu/packing/index.html
>
> Pick structure from the left menu and then click the “Show Contents of One
> Unit Cell”. Works beautifully!
>
> The commands are:
> display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP unitcell
> 'cpk'; spacefill 1%;
>
> Dean Johnston
>
> On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu) wrote:
>
>
> Can the "slab" command be used to produce presentations equivalent to the
> image linked below?
>
> https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/
> File:CCC_crystal_cell_(opaque).svg
>
> If so, any suggestions on how to do that would be appreciated.
>
> Thanks,
>
> PM
> 
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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] Jmol 14.13.1

2017-04-10 Thread Otis Rothenberger 
Pshemak and Dean,


Back in the day, I was just an organic chemist who had to prove to my X-ray 
colleagues that my molecule was worthy of their efforts (data returned on punch 
cards). Consequently, I admit to a weak point explaining my tests below on 
Pshemak's file. But here goes:

On both  Pshemak's Na file and COD 9008545 (Na), I need to do the entire 
following script to get a correct body-centered cubic JSmol image.

save orientation;load "" {1 1 1} ;set displayCellParameters false;restore 
orientation;center;display unitcell; spacefill ionic 100%; lcaocartoon scale 
1.0 CAP unitcell 'cpk'; spacefill 1%;

By the way Dean, that spacefill 1% is a slick trick. I was just turning 
spacefill off - not satisfactory.

I have an in this day (not back in the day) X-ray  colleague  at ISU. I'm going 
to ask him for an explanation of why "display unitcell" has to operate on {1 1 
1}, but I suspect that Bob can answer this question.

Otis

--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org

> On Apr 10, 2017, at 2:02 PM, Pshemak Maslak  wrote:
> 
> Otis and Dean,
> 
> I just tested NaCl in JSmol (JavaSript) on a rather old version (14.4.1). 
> Surprise: it works as intended (no freezing).
> 
> I will do more testing. 
> 
> Otis, I will send you the cif files to your address (list does not allow 
> attachments).
> 
> Thanks,
> 
> PM
> 
> On 4/10/2017 1:49 PM, Otis Rothenberger wrote:
>> Dean and Pshemak,
>> 
>> First, OK I'm a believer. The command "display unitcell" is real, and it's 
>> neat. It cuts off all of the exterior atoms (to unit cell). That's good to 
>> know.
>> 
>> On the desktop app issue, I think I was one of the early users to say 
>> good-bye to Java. I'm a small molecule guy, and Bob saved me with JSmol. As 
>> a small molecule guy, I can get away with my no-Java approach. 
>> 
>> Unfortunately, I can't be of much help with Java app questions.
>> 
>> On your final question, can you send me (point me to) the CIF file? I'm 
>> assuming from the context of this question that this is the JSmol version. 
>> Is that correct?
>> 
>> Otis
>> 
>> --
>> Otis Rothenberger
>> o...@chemagic.org 
>> http://chemagic.org 
> 
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Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Robert Hanson 
OK, I know how I my comparison method violated the general contract. Very
surprised this ever worked!

On Mon, Apr 10, 2017 at 1:37 PM, Robert Hanson  wrote:

> Pshemak,
>
> Gotta love this error message:
>
> java.lang.IllegalArgumentException: Comparison method violates its
> general contract!
>
> I'll check on this.
>
> Bob
>
>
> On Mon, Apr 10, 2017 at 12:21 PM, Pshemak Maslak  wrote:
>
>> Otis and Dean,,
>>
>> Thanks for the explanation. I was indeed able to find the whole command
>> (spacefill ionic;lcaocartoon scale 1.0 CAP unitcell "cpk";spacefill off
>> *) * in the documentation (in the "cpk" example of lcaoCartoons).
>>
>> I think I understand it better now. The "spacefill" spheres are replaced
>> with "cpk" spheres" which then are SLAB-ed (CAP-ed really) using "unitcell"
>> as slabbing planes.
>>
>> I tried it on NaCl (cif file). It works on a cell containing one Cl-  in
>> the center of the cell and one Na+  in the corner (which is properly
>> CAP-ed).
>>
>> However when I load {1 1 1} cell to get all ions within the cell, the
>> Jmol (desktop Java app) freezes. I tried the newest version (14.13.1) an an
>> older one (14.8.0) with the same results.
>>
>> I tried  Na (cif)  (loading {2 2 2} and using "display unitcell" (which
>> show all needed atoms), but "lcaocartoon scale 1.0 CAP unitcell
>> "cpk";spacefill off"  froze Jmol as well.
>>
>> Any suggestions?
>>
>> Thanks for your help.
>>
>> PM
>>
>>
>>
>> On 4/10/2017 12:08 PM, Otis Rothenberger wrote:
>>
>> Pshemak,
>>
>> The CAP part is discussed here:
>>
>> https://chemapps.stolaf.edu/jmol/docs/index.htm?=
>> 1=14.6#isosurface
>>
>> Scroll down until you see CAP listing.
>>
>> The spacefill 1% is just hiding the atoms leaving the lcaocartoons
>>
>> Dean, the main reason I'm jumping in here is the display unitcell
>> command. Is that a legal Jmol Script command? After loading a CIF file, I
>> thought that you had to do something like this to get the unit cell:
>>
>> save orientation; load "" {444 666 1}; set displayCellParameters
>> false;restore orientation; unitcell on; display cell=555; center visible;
>> zoom 200;
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> o...@chemagic.org
>> http://chemagic.org
>>
>> On Apr 10, 2017, at 11:44 AM, Pshemak Maslak  wrote:
>>
>> Thank you Dean,
>>
>> I do not understand the
>>
>> lcaocartoon scale 1.0 CAP unitcell 'cpk'; spacefill 1%;
>>
>>
>> part of the command. Is it documented in https://chemapps.stolaf.edu
>> /jmol/docs/  ?
>>
>> Thanks,
>>
>> PM
>>
>>
>> On 4/10/2017 10:46 AM, Dean Johnston wrote:
>>
>> Yes - I have an example at: http://crystals.otterbein.
>> edu/packing/index.html
>>
>> Pick structure from the left menu and then click the “Show Contents of
>> One Unit Cell”. Works beautifully!
>>
>> The commands are:
>> display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP
>> unitcell 'cpk'; spacefill 1%;
>>
>> Dean Johnston
>>
>> On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu) wrote:
>>
>>
>> Can the "slab" command be used to produce presentations equivalent to the
>> image linked below?
>>
>> https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/F
>> ile:CCC_crystal_cell_(opaque).svg
>>
>> If so, any suggestions on how to do that would be appreciated.
>>
>> Thanks,
>>
>> PM
>> 
>> --
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>> engaging tech sites, Slashdot.org ! http://sd
>> m.link/slashdot___
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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




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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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Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Pierluigi Quagliotto 

Dear Bob,

many thanks for the crucial update!

Yesterday I have published on the site the page for the step-by-step 
chirality assignment procedure.


It should be intended for compound having only one chiral carbon since I 
did not implemented yet any function to take into account the presence 
of more chiral carbons.


the page which is present on the development site (only in italian) is 
working correctly with the "unofficial" jsmol.zip you prepared and gave 
us before making the finale 14.12.1 release.


http://5.135.186.232/STdM/index.php/it/esercizi/esercitarsi-sulla-chiralita

while the page on the production site, running the 14.13.1 version, is 
showing an error for a call to a function:


[Javascript] The required class file

/jsmol/j2s/JU/BNode.js
could not be loaded. Script error. Syntax Error. and other things are 
following.


Did I write something in the scripts that now should be treated and 
written in another way? Or this is a bug?




Many tahnks ina dvance for your help!

Bye!

Pierluigi




Il 10/04/2017 04:44, Robert Hanson ha scritto:

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



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Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Pierluigi Quagliotto 

Dear Bob,

Sorry... I forgot to add  the address of the production site:

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

bye!

Pierluigi

il 10/04/2017 04:44, Robert Hanson ha scritto:

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



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Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Pshemak Maslak 


Can the "slab" command be used to produce presentations equivalent to 
the image linked below?


https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg 



If so, any suggestions on how to do that would be appreciated.

Thanks,

PM
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Re: [Jmol-users] Jmol 14.13.1

2017-04-10 Thread Dean Johnston 
Yes - I have an example at: http://crystals.otterbein.edu/packing/index.html

Pick structure from the left menu and then click the “Show Contents of One
Unit Cell”. Works beautifully!

The commands are:
display unitcell; spacefill ionic 100%; lcaocartoon scale 1.0 CAP unitcell
'cpk'; spacefill 1%;

Dean Johnston

On April 10, 2017 at 9:00:03 AM, Pshemak Maslak (p...@chem.psu.edu) wrote:


Can the "slab" command be used to produce presentations equivalent to the
image linked below?

https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_(opaque).svg

If so, any suggestions on how to do that would be appreciated.

Thanks,

PM
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