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 <hans...@stolaf.edu> 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 <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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