input format 4

pure xyz data

such a file contains only three columns with X Y Z values (separated by spaces)

You cannot calculate diffraction patterns from such a file. If JSV does seem to calculate a diffraction pattern then this would actually be for a previously loaded structure of which the temporary file tmp.ucc is still present in the directory.

If the scale of the XYZ data is other then the usual unit cell coordinates (0.0-1.0) then the atom radii might appear unreasonably large/small. A possible solution would be to write a cartesian_cell file, in which you can change the lattice constant a for a scaling.

Since no atomic number nor atom radius is given to atoms from pure xyz data,
JSV assigns the atomic number 106 to them. So if you want to change the radius and color of atoms from a xyz file you have to change the properties of element 106 (Uh) under [Option] [atom radii/colors].