Karl, this is great! Congratulations. I'm delighted the connect command
is working so well for you.
Suggestion to compact it a bit:
1) you don't need "1.0" unless you really think there are connections
shorter than that that you DON'T want to bond.
2) You no longer need to select, but if you use it, you don't have to
specify it over and over. The following should work:
select *;
connect 2.7 (oxygen) ;
connect 3.0 (fluorine) ;
connect 2.9 (bromine);
connect 3.0 (iodine);
connect 3.3 (sulfur or selenium) ;
connect 2.9 (sodium) (chlorine);
connect 3.8 (caesium) (chlorine);
(if that wasn't in 10.00.48, it's in
http://www.stolaf.edu/people/hansonr/jmol/test/json)
3) putting those radio buttons in a select box would be friendier! :)
4) for polyhedra, I'd select one or the other of the elements such as Na
or Cl, but not both. That way they won't overlap. One possibility would
be to select all the anions prior to the polyhedrons command:
select chlorine or fluorine or .....
polyhedra bonds
5) for fun, I just modified the polyhedra command so that it allows you
to specify the number of bonds to allow. so if you say
polyhedra bonds 6
then ONLY octahedra will show. Does that sound useful?
Something else that might be useful: since connect can dynamically
change the bonding, you can now connect some atoms, create polyhedra,
unconnect them, connect others, make new polyhedra, etc.
If you find that aspects of the polyhedra command need improvement,
please do ask. I'm VERY interested in this.
Bob Hanson
Karl Harrison wrote:
The recent discussion about crystal and minerals and JMOL polyhedra
has been very interesting to me since this is an area I'm have been
working on visualizing.
I offer here a web to help testing polyhedra and connect command.
<http://www.chem.ox.ac.uk/ic4/polyhedratest.asp>
There are >300 different structures available for testing.
Most seem to display fine, though there a few exceptions, most
notably NaCl and structures of the same lattice type.
The code I use is as follows:
var script = "load ./inorganicmodels/" + model + ";
select *; connect DELETE; select *; connect 1.0 2.7 (oxygen); select
*; connect 1.0 3.3 (sulphur); select *; connect 1.0 3.3 (selenium);
select *; connect 1.0 3.0 (fluorine); select sodium; connect 1.0 2.9
(chlorine); select caesium; connect 1.0 3.8 (chlorine); select *;
connect 1.0 2.9 (bromine); select *; connect 1.0 3.0 (iodine);
select *; polyhedra bonds; select *; polyhedra frontedges; wireframe
off; select silicon; colour blue; select *;connect; wireframe on;
select *";
The following is my explanation of why I have used the above code,
please feel free to correct me if my reasons are wrong since this
will very much help me fix the problem structures. I'm not really
convinced of the following arguments, because several structures do
not show the expected behavior.
var script = "load ./inorganicmodels/" + model + "; - the load
code, all my structures are .pdb files, I couldn't get JMOL to
display the .cif files I wanted they were created in Crystalmaker
select *; connect DELETE; - remove all connections so I can start
a fresh
select *; connect 1.0 2.7 (oxygen); - select all and connect them
within distance to oxygen, similar for the anions below
select *; connect 1.0 3.3 (sulphur);
select *; connect 1.0 3.3 (selenium);
select *; connect 1.0 3.0 (fluorine);
select *; connect 1.0 3.0 (iodine);
select *; connect 1.0 2.9 (chlorine);
select caesium; connect 1.0 3.8 (chlorine); a special case but
didn't help
select *; connect 1.0 2.9 (bromine);
select *; polyhedra bonds; - now this I assume then connect all
using polyhedra if possible based on the connection made above.
select *; polyhedra frontedges; - make pretty
select silicon; colour blue; - now make pretty silicon
select *;connect; - now connect all based on built-in bonding rules
wireframe on; - make wireframe connections for remaining atoms not
connected via polyhedra.
select * - select all so the buttons below model are active for all
atoms
To me the above sort of makes sense, but the AgCl looks okay but why
not LiCl or KCl and NaCl has a lot of extra polyhedra, these are at
the edges and are made up of distorted tetrahedrons, there are
several structures like this.
The structure of Y Ba Cu Oxide the superconductor
(fig2330bYbcopoly1.pdb) doesn't much sense either, it has several
flat square planes which is correct but why not the correct number.
Anyway this message is long enough have a look and feel free to
correct my JMOL script errors.
Regards, Karl
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