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 <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
>>
>> <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 <mailto:o...@chemagic.org>
>> http://chemagic.org <http://chemagic.org/>
>>> On Apr 10, 2017, at 11:44 AM, Pshemak Maslak <p...@chem.psu.edu
>>> <mailto: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/
>>> <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
>>>> <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
>>>> <mailto: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
>>>>>
>>>>> <https://en.wikipedia.org/wiki/Atomic_packing_factor#/media/File:CCC_crystal_cell_%28opaque%29.svg>
>>>>>
>>>>> If so, any suggestions on how to do that would be appreciated.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> PM
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