Use of NLOPredict

Suppose we perform a resonant SHG experiment on a thin film of NMA.  Suppose also that we collect psp and sps polarized light from the sample.  We would like to relate the signal we gather in the lab frame back to the molecular frame to determine the NMA's orientation in the thin film using NLOPredict.

First, download NMA.pdb and Amide_I.cfg from http://nlopredict.sourceforge.net/.
Then, launch UCSF Chimera.  Once Chimera has opened, we need to import the molecule.
Chimera: File -> Open -> NMA.pdb
The NMA molecule should now be visible in the Chimera window.

Now we need to start the NLOPredict plug-in.
Chimera: Tools -> Indiana/Purdue -> NLOPredict
A new window should open and a message saying "updating contour plots" should appear.
Note:  you will also need to toggle on the Plot -> Single Molecule Mode

Now we import the non-linear optical data for the NMA molecule into NLOPredict.
NLOPredict: File -> Import -> .cfg File -> Amide_I.cfg

We make sure NLOPredict is set to SHG mode.
NLOPredict: Params -> Multiplication order -> mu*alpha (SHG)

It's time to have a look at the beta tensor. There are two visualization methods; one based on sagittary representations indicating the principle moments of the alpha tensor and the transition moment, and a space-filling representation. To view the sagittary representation, select: 
NLOPredict: View -> alpha/mu visibility -> magnitude
A set of single-sided and double-sided arrows should appear, representing the transition moment and the eigenvalues of the alpha tensor, respectively.
NLOPredict: View -> alpha/mu visibility -> surface
An ellipseoid should appear in the Chimera window, superimposed over the NMA molecule.

Quantitative connections between the molecular frame and the laboratory frame can be facilitated using the contour plot functions in NLOPredict.
NLOPredict: Plot -> contour plot
NLOPredict: Params -> Adjust Contour Plot
Contour Editor: Change color map to Jet
Contour Editor: Change upper plot to “abs(sps)**2”
Contour Editor: Change lower plot to “abs(psp)**2”
Contour Editor: Click Apply
Contour Editor: Click Close

These entries will generate plots of the expected intensities for the SPS and PSP polarization combination (where the first index corresponds to the polarization state of the exigent beam, and the second and third correspond to incident polarization states). Any supported mathematical combination of Jones or Cartesian tensor elements can be plotted, depending on the nature of the experiments.
Clicking on the contour plot areas will rotate the molecule in Chimera to match the molecular orientation that produces the data point on the contour plot.  In the case of NMA, obviously there is more than one possible orientation capable of satisfying a unique set of psp and sps signals. You can either export the entire contour plot, or export the complete set of Cartesian and Jones tensor elements for a particular molecular orientation (both as text files) using the Export option under NLOPredict:File->Export 

Opening the file generated by exporting the tensor, we can find the values for the molecular Beta tensor, Cartesian Chi's and Jones Chi's.