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/
> File: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
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