Molecular model building and modelling using Jmol

By default, Jmol is set to an enhanced model building mode (Virtual Model Kit or VMK).

This button: will remove the model building mode and instead open a file dialog to read a .cif (or other recognised molecule 3D coordinate) file and will save a resulting spacefill representation as a VRML file (.wrl) suitable for e.g. 3D printing.

This button: will remove the model building mode and instead open a file dialog to read an orbital .cub file, render the result at 0.02au and will save the model as a VRML file. The .cub file should be generated using e.g. Gaussview.

This button: will remove the model building mode and instead open a file dialog to read an orbital .cub file, render the result at 0.01au and will save the model as a VRML file. The .cub file should be generated using e.g. Gaussview.

This button: will remove the model building mode and instead open a file dialog to read an orbital .cub file, render the result at 0.005au and will save the model as a VRML file. The .cub file should be generated using e.g. Gaussview.

This button: will remove the model building mode and instead open a file dialog to read an orbital .cub file, render the result at 0.005au and will save the model as a VRML file. The .cub file should be generated using e.g. Gaussview.

This button: will remove the model building mode and instead open a file dialog to read an orbital .cub file, render the result at 0.005au and will save the model as a VRML file. The .cub file should be generated using e.g. Gaussview.

This button: will remove the model building mode and instead open a file dialog to read an orbital .cub file, render the result at 0.005au and will save the model as a VRML file in yellow/green. The .cub file should be generated using e.g. Gaussview.

This button: will remove the model building mode and instead open a file dialog to read an orbital .cub file, render the result at 0.005au and will save the model as a X3D file. The .cub file should be generated using e.g. Gaussview.

Generating the .cub file

1. Run a Gaussian calculation in the normal way (on the HPC system) and download the .fchk file
2. If you instead want to display NBO bond (localised) orbitals, put

   pop(nbo,savenbos)
   

   as a keyword for the Gaussian calculation
3. Double click the .fchk file on your computer and Gaussview will open. In Edit/MOs, select the MOs you want, and Visualize/update.
4. In Results/Surfaces/Contours highlight an orbital, and from Cube actions, invoke save. You can set the cube to course, medium or fine to increase resolution.
5. You can of course also generate a .cub file using the utility cubgen directly, via the command line.

H. S. Rzepa, July 1, 2013