[Jmol-users] Playing with isosurfaces for ionic structures with 10.9.72

[Alan H. <he...@il...>]

I am continually delighted by how fast this is moving. I no sooner think
of something new I would like to do, and Bob has already implemented it.
In particular I have updated ICSD to 10.9.72 with ionic isosurfaces and
have been experimenting.

1) A zeolite structure such as:
http://icsd.ill.fr/icsd/index.php?action=Search&authors=henry&mineral=zeolite
is displayed with default polyhedra. If I click on "cavities" to do:
isosurface ionic solvent;
I get a nice drawing showing a surface that surrounds the atoms leaving
big holes for the cavities, which is very clear if I set the atoms to 0%
and turn off bonds and polyhedra.

2) A synroc (hollandite) structure such as:
http://icsd.ill.fr/icsd/index.php?action=Search&authors=burr&mineral=hollandite
Now "cavities" does not show much because they are occupied by nitrogen
(and unlocated hydrogen). But I can ignore the nitrogen (I have to find a
way to do this with my simple atom-select interface).
isosurface ionic ignore(nitrogen) solvent;
which shows very nicely the cavities available for NH4 or other cations.

However 2) also shows partial surfaces surrounding oxygen, so I wondered
what I would see if instead I ignored oxygen:
isosurface ionic ignore(oxygen) solvent;
Wow ! That is very interesting. It draws surfaces enclosing the remaining
atoms, N and Mn. (I switched off the bonds and polyhedra to see that).
This is a kind of a "reverse solvent surface" and is very instructive for
inorganic materials which can often be thought of as a lattice of oxygen
(or other big anions) with the cations in the holes. Here I have a way of
seeing those holes in th anion lattice (which is what I have been going on
about without being understood :-)

Wouldn't it be nice if I had a "reverse isosurface" switch :-)

There are so many possibilities already (most of which I have not yet
discovered). And it is very, very nice that I can now use the up/down
arrows in the console to recall previous commands, edit them and re-issue
them. (Even if most ICSD users would never get as far as the console :-)

BTW, I found a way to re-route the output of the AMS mineralogical
database through the ICSD interface so that finally it now draws polyhedra
and isosurfaces etc (click on "Search also the AMS database" at the bottom
of the ICSD search form - the output looks like it comes from AMS, but it
was slightly doctored on the way :-)  Is Bob Downs listening here ?

Alan.