c2x and Jmol

Jmol is a particularly nice program for being written in Java, and hence very portable, and also remarkably fast. The example here uses the calculation on ethene from the Xcrysden example.

Jmol likes 3D data to be in .cube files, which also contain the atomic positions. Simply reading a .cube file using the File menu reads only the atomic data. To produce an isosurface, one must open the script window from the file menu, and type a whole command, such as:

isosurface rho cutoff 0.5 "ethene.cube"

The label, "rho", can be almost anything, except certain keywords. Beware that "charge" is a prohibited keyword here, as is "sigma".

Jmol can plot multiple isosurfaces simultaneously, either different values from the same dataset, or from different datasets. Thus to plot psi with phase, and showing both the carbon-carbon σ bond and the π bond, one can first produce suitable cube files with c2x,

$ c2x --cube -b=1 ethene.check ethene.b=1.cube
$ c2x --cube -b=6 ethene.check ethene.b=6.cube

and then, in Jmol's console,

  load "ethene.b=1.cube"
  [rotate to taste]
  isosurface sig cutoff 0.5 "ethene.b=1.cube"
  isosurface pos cutoff 0.3 "ethene.b=6.cube"
  isosurface neg cutoff -0.3 "ethene.b=6.cube"
  color $sig yellow


Ethene sigma and pi bond

Finally, if printing from Jmol, remember to set the background to white. This can be achieved by right-clicking on the canvas, and selecting Color, Background, White. Jmol is not very good at compressing its png and pdf images, so exporting to png and using bmp2eps is probably the best way of getting png, pdf and eps images from Jmol. Using JPEG is unlikely to be satisfactory, unless you like fuzzy edges around your atoms.