The good news is that this is our software, which means that we can customize practically everything about it: colors of the atoms, bonds, and orbitals, sizes of everything, background color, bounding boxes and more. The bad news is that this is still under development, and currently is not as easy as it will ultimately be.
Notice: This is developmental software! Use at your own risk!!
% /ul/rpm/python/plotsection.py (output file name)where (output file name) is the name of the output file that generated the restart file you wish to visualize. This will give a decent &plot section that can be appended to the end of your restart file. Replace the question marks with the orbital you wish to see. Now run this restart file. This should only take a minute, because Jaguar does not rerun the job, it simply evaluates the wave function on the specified grid.
The source code to the plotsection script is available here. There's nothing magic, or even necessarily correct, about the script, and if you feel like rewriting it with different parameters, by all means do so.
% /ul/rpm/python/orbviewer.py (plot file name)The plot file name should be the same as the restart file name, with '.plt' appended to it instead of '.in'. The source code to the orbital plotting script is available here. Feel free to experiment!