Re: [Jmol-users] help: required Jmol file formats

[Miguel <mi...@jm...>]

> Hi,
>
> Does Jmol have an internal file format where one can specify an atom
> location XYZ (Cartesian) and the radius of the sphere it will use to
> represent it, ie. adjust it's Van der Waals radius?
>
> I want to display a set of overlapping spheres of varying
> diameter.  Unfortunately, the geomview applet, JGV, does not display
> spheres and so I was hoping to use Jmol for this task.

Martin,

Using the scripting language you can easily adjust the color and diameter=

of every sphere.

I suspect that the simplest format for you to use would be the .xyz forma=
t:

-----
Martin's test file
3
H 0 0 0
H 1 1 1
H -1 -1 -1
-----

First line is a comment
second line is atom count
subsequent lines are element symbol followed by cartesian coordinate
values x, y, z expressed in angstroms.

You can then set the colors and sizes as follows:

select atomno=3D1; color atom red; spacefill 0.5;
select atomno=3D2; color atom green; spacefill 1.0;
select atomno=3D3; color atom blue; spacefill 2.0;

This is setting the colors to be red, green, and blue and the radii to
0.5, 1.0, and 2.0 angstrom, respectively.

Do not forget to use a decimal point in the sizes or you will get
unexpected results.


Let us know how it works out.


Miguel