> 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 format: ----- 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=1; color atom red; spacefill 0.5; select atomno=2; color atom green; spacefill 1.0; select atomno=3; 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 ------------------------------------------------------- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space? Enter now for the Oracle Space Sweepstakes! http://ads.osdn.com/?ad_ids93&alloc_id281&op=click _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
