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 <mailto:o...@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
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
<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
If so, any suggestions on how to do that would be appreciated.
Thanks,
PM
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