A short note on how to use gOpenMol

What you need to do with gOpenMol:

1. read the gOpenMol.xyz file by going to: File -> Import -> Coord -> Browse -> Apply; you should see your system in the main graphical window as connections between atoms
2. read in the gOpenMol.cube file by going to: Run -> gCube2plt/g94cub2pl (cube) -> Browse -> Apply ; it will open a window and will produce an output in it finished by "Job done ..."; a file gOpenMol.plt will be produced
3. then plot the density by reading the gOpenMol.plt file: Plot -> Contour -> Browse -> Import File. In a new window openned, you will find the minimum and the maximum values of the density; choose the density value in the boxes underneath the min/max info and click Apply: the density will be shown alongside the atomic positions in the graphical window where you will be able to rotate it
4. To make the density transparent, click on Details opposite the chosen density level and change the Opacity level, then click Apply. It is possible to plot several density levels in the same way by filling in several density levels and then changing their opacities.
5. To see atoms better, use: View -> Atom Type and then the option Licorice with e.g. Cyl.rad = 0.1 and Sph. rad. = 0.3. To have different radii for different species, use CPK as well. See the gOpenMol manual for more instructions. gOpenMol is freely available at: http://www.csc.fi/gopenmol/
6. To save a file with the picture in the graphical window, use: File -> Hardcopy -> Apply

An example of the gOpenMol image is shown in Fig. 3.7.

Figure 3.7: Surfaces of constant density for an adenine molecule on gold: side (left) and top (right) views.

Two transparent surfaces are shown.