Management of 3D stripes

Here we give step-by-step instructions on how to customize your iNMR installation for 3D spectroscopy. At the end you'll be able to generate 3D stripes corresponding to an ensemble of selected 2D peaks and to change the order of the stripes afterwards. You are kindly invited to read the general introduction to customization before this article.

The setup is now complete. We also advise to work on partial submatrices instead of your original 3D spectra, because this measure easily translates into a 10 times speed boost. To create a submatrix, first process a 3D, including baseline correction, then use the command Export. A new file will be created.

Open your spectra and the console. Check the option for all documents. Without it, pp2s does nothing. Perform a selected peak-picking on a 2D spectrum. For each picked peak a stripe will be created. This means that your list of picked peaks must be conveniently short. The script pp2s is very simple and has the following limitations:

Now press the button “pp2s” you had created before.

To change the width of all stripes, e.g. to 0.1 ppm, type:

STRIPE_WIDTH = 0.1

Then repeat the command pp2s. To swap the position of the second and third stripe, type:

STswap( 2, 3 )

To change all the positions, type, for example:

STorder( 3, 2, 1 )

In the last given example you have reverted the order of 3 stripes. To operate on a single stripe, press the key “7” repeatedly until you see a frame around the desired stripe. You can, optionally, press “*” or other keys to refresh the screen at this point. You can perform peak-picking on each stripe, set different contour levels (or colors) for each stripe, etc... To draw an arrow from a stripe to another, it must be of the type document note. If you want to preserve a certain configuration of stripes, use the command Page/Add Page. Pages add yet another dimension, and they are fast to switch through.

You might want to edit (or, at least, read) the program pp2s and the function STswap and STorder or to create new functions. Why? For example, they assume that the x axis of each spectrum correspond to the same nucleus. You may need something more general or more specific. You can split the program in two and avoid using the “for all documents” option. You can use another 3D spectrum as the source of the peak-picking list. Most of all, you can set your own default value for STRIPE_WIDTH.


 
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