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 <hans...@stolaf.edu> 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 <p...@chem.psu.edu> 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?&fullmanual=
>> 1&ver=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 <p...@chem.psu.edu> 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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>
>
> --
> 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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