MATLAB program for quick 2D NMR processing. Requires the raw bruker data for the 1D and 2D spectra as generated by TopSpin. Requires MATLAB 2019a and later for the readmatrix function.
BEFORE USING THE PROGRAM, CHANGE THE VARIABLE "savelocation" TO YOUR DESIRED FOLDER TO SAVE THE FIGURES INTO. INSTRUCTIONS AT THE TOP OF THE CODE.
Use the data browser to select the experiment number folder folder for the 2D data in the "Input 2D Folder", e.g. "usr/NMRdata/Sample_A/1/". If you want to plot externally acquired spectra on the axes rather than the internal skyline projection, select "External Projection" and use the data browsers to select the experiment folder for the 1D data. Proc no. is assumed to be 1 here.
Choose the nuclei in the dropdown boxes for the2 axes, these are coded to assume a reasonable scale for the selected nucleus and name the axis accordingly. More can be added upon request, or you can add your own. Limits can be edited in the provided boxes.
Once data is in, click "Load Data".
Next use the sliders to select a threshold factor, and number of contour levels, then push "Plot". The spectrum will plot in a new window after a few seconds, if you want to change the threshold factor (I've found this to be trial and error depending on amount of signal), or number of contour levels you can just push "Plot" again and a new figure will appear (without replacing the old one).
After generating a figure you like, input a desired file name into the "Input Save File Name" box and push the "Save" button.
Troubleshooting:
- If you're trying to plot a 2D with a proc. no. higher than 5, you can either add more options into the curly brackets on line 69, or in topspin just use the au program "wrp" and choose a number from 1-5. Usually it should be proc. no. 1.
- If you're having trouble saving, ensure that the variable "savelocation" is equal to a real PATH to a folder. The default is set as ~ which should be the home directory.
- If the progam can't find a real path for the F1 dimension spectrum (either because it's a bad path or you just didn't put it) there will be a message in the command line, both when you load data and when you plot the graph.
- If you don't input correct paths for the F2 dimension or the 2D data, there will also be a message in the command line, then an error will show.
If you still have issues, feel free to contact me at [email protected].