Nick Greeves wrote:
> Hi All,
> We have been trying to use Jmol to display coordination polyhedra for
> a range of inorganic structures and have encountered what seems to us
> anomalous behaviour. I have set up some of the pages on an external
> server using Jmol 11.6RC6 so that anyone interested can take a look.
> These pages are unfinished and may disappear without warning. I
> suspect some of these may require expert input from Bob but others may
> sound familiar to other users.
>
> NiAs <http://osxs.ch.liv.ac.uk/~ng/sandbox/
> <http://osxs.ch.liv.ac.uk/%7Eng/sandbox/>_NiAs-test.htm>
> <http://xserve.ch.liv.ac.uk/%7Eskho/_NiAs-test.htm>
> 1st "Ni Polyhedron" button
> why is third octahedron not visible?
> perhaps the code "restrict cell={2 2 2}; set unitcell {1 1 1}; centre
> unitcell; polyhedra 6 ((_ni) and visible); colour polyhedra
> translucent; zoom 200" only works properly when the polyhedra are
> inside the cells, and not when the polyhedra overlaps into a second cell?
Only two Ni in cell {2 2 2} have 6 As around them. The third is in cell
{1 1 1}
>
> Li3Bi <http://osxs.ch.liv.ac.uk/~ng/sandbox/
> <http://osxs.ch.liv.ac.uk/%7Eng/sandbox/>_Li3Bi(2)-test.htm>
> <http://xserve.ch.liv.ac.uk/%7Eskho/_Li3Bi%282%29-test.htm>
> Various attempts at showing BOTH the tetrahedra and octahedra for both
> types of Li.
> Perhaps problems displaying 2 types of polyhedra of the same element
> (Li) together (changing colours or translucent/opaque)
> also, an example where polyhedra do not extend beyond unitcell (notice
> missing Oh polyhedra on one side)
Polyhedra won't go to atoms that are not there. The thing to do is start
with
select _li and connected(4)
or
select _li and connected(6)
then do the polyhedra -- with different colors. I found it worked to use
select _li and connected(4) and atomno < 30;polyhedra 4 red
select _li and connected(6) and atomno > 50;polyhedra 6 green
that way you get some spacial separation as well.
>
> YCl3 <http://osxs.ch.liv.ac.uk/~ng/sandbox/
> <http://osxs.ch.liv.ac.uk/%7Eng/sandbox/>_YCl3(2).htm>
> <http://xserve.ch.liv.ac.uk/%7Eskho/_YCl3%282%29.htm>
> BiI3 <http://osxs.ch.liv.ac.uk/~ng/sandbox/_BiI3(2).htm>
> <http://xserve.ch.liv.ac.uk/%7Eskho/_BiI3%282%29.htm>
> These use code "hideNotselected", to hide unwnated ions but how can we
> select polyhedra as well so they show up?
OK, so I see:
select *; hide none; centre; boundbox off; unitcell off; axes off;
wireframe off; spacefill off; polyhedra off; polyhedra 6 (_Bi) to (_I)
collapsed edges; select atomno=261 or atomno=213 or atomno=111 or
atomno=264 or atomno=161 or atomno=113 or atomno=3 or atomno=164 or
atomno=57 or atomno=272 or atomno=221 or atomno=119 or atomno=169 or
atomno=172 or atomno=171 or atomno=121 or atomno=13 or atomno=67 or
atomno=70 or atomno=69 or atomno=227 or atomno=230 or atomno=229 or
atomno=280 or atomno=127 or atomno=130 or atomno=129 or atomno=180 or
atomno=21 or atomno=285 or atomno=239 or atomno=137 or atomno=288 or
atomno=185 or atomno=139 or atomno=31 or atomno=188 or atomno=83 or
atomno=296 or atomno=247 or atomno=145 or atomno=193 or atomno=196 or
atomno=195 or atomno=41 or atomno=147 or atomno=93 or atomno=96 or
atomno=95 or atomno=253 or atomno=256 or atomno=255 or atomno=304 or
atomno=153 or atomno=156 or atomno=155 or atomno=204 or atomno=49 or
atomno=143 or atomno=240 or atomno=291 or atomno=140 or atomno=192 or
atomno=39 or atomno=191 or atomno=35 or atomno=92 or atomno=257 or
atomno=259 or atomno=260 or atomno=157 or atomno=159 or atomno=160 or
atomno=305 or atomno=207 or atomno=56 or atomno=205 or atomno=107 or
atomno=152 or atomno=297 or atomno=199 or atomno=197 or atomno=200 or
atomno=48 or atomno=99 or atomno=97 or atomno=100 or atomno=117 or
atomno=214 or atomno=267 or atomno=114 or atomno=168 or atomno=11 or
atomno=167 or atomno=7 or atomno=66 or atomno=231 or atomno=233 or
atomno=234 or atomno=133 or atomno=131 or atomno=134 or atomno=183 or
atomno=281 or atomno=28 or atomno=181 or atomno=81 or atomno=74 or
atomno=71 or atomno=73 or atomno=20 or atomno=173 or atomno=176 or
atomno=175 or atomno=126 or atomno=273; set hideNotSelected TRUE; hide
hidden and not polyhedron; spacefill 12%; centre [_Bi] 5; show centre;
centre; zoom 120
but " hide hidden and not polyhedron" does nothing, because "polyhedron"
is not defined (I think). I wouldn't use hideNotSelected here. Why not
just say, for example,
select _Bi;polyhedra 6;hide not connected(6)
>
> Then using Jmol.jar to view close-packed structures and hoping to
> display the holes in ccp, hcp, and bcc (attached) leads to many problems.
> The command "within.... {atomno= }" seems to only display exterior
> holes rather than internal ones.
>
within what?
> And using command "isosurface interior cavity ___ ", hcp are holes
> displayed, but cannot find code to display any holes in ccp.
>
that is definitely a challenge.
> For bcc,
> isosurface interior cavity 0.001 within 5.0 (atomno=11) sasurface 0.04
> isosurface interior cavity 0.05 within 5.0 (atomno=11) sasurface 0.04
> isosurface interior cavity 0.01 within 5.0 (atomno=11) sasurface 0.04
> holes shown are quite small, and only shown on the surfaces of the
> unit cell only.
> There is no difference observed when "within" parameter omitted
> isosurface interior canity 0.01 sasurface 0.02
I think cavities are mostly just for zeolites. I don't know... I would
say spacefill is still your best bet for showing these.
> Bob
>
>
> We would welcome any ideas or solutions.
>
> All the best
>
> Nick
>
> --
>
> 3D Organic Animations http://www.chemtube3d.com
>
> Tel: +44 (0)151-794-3506 (3500 secretary)
>
>
>
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--
Robert M. Hanson
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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