3D examples in Bruker format (courtesy of the University of Florence)
Prof. Mario Piccioli (CERM, University of Florence) has generously provided an assorted set of 3D spectra of a metalloprotein (the reduced form of copper, zinc superoxide dismutase from Salmonella enterica). They are listed at the bottom of this page. The NMR resonances have been almost completely assigned and deposited at the BMRB archive. Other authors are: Beatriz Jimenez, Mirko Mori, Andrea Battistoni and Marco Sette. I want to thank them all for the very nice spectra. Please note that they are not responsible for this web site and for the way the files have been packaged.
You have the opportunity to learn and process these 3D data sets with the program of your choice. (Assuming you are already expert in 2D processing with the same program!). The original, unprocessed, Bruker data sets are furnished. Processing parameters (in the iNMR format) are also included as separate “plist.inmr” files. It means that, if you open the spectra with iNMR, it will automatically process them. The given processing parameters are merely indicative. They don't come from the cited owners and authors. This is work in progress and better parameters can be enclosed in future. The present parameters can be completely wrong. If you are curious about which processing iNMR performs on each spectrum, select the command “Edit/Copy.../Processing”, then paste into an empty page (or into the spectrum). The list of performed actions will appear. You are free to reload the FID (command: “File/Reload”) and apply the processing of your choice.
3D processing is RAM-thirsty. If your computer is forced to “swap” memory pages, then everything will become painfully slow. It can be avoided by quitting the unused applications. A more essential rule is to never combine zero-filling (or LP filling) with the hyper-complex option. Beware that iNMR by default turns on both zero-filling and the hyper-complex option! You must disable one of them manually (unless you keep the processing proposed hereby, of course).
The purpose of this site is also to demonstrate the 3D capabilities of iNMR and iNMR reader. Both programs can be freely downloaded. The processing parameters I am proposing for these five experiments can be used for different spectra acquired with the same pulse sequences. Weighting functions and other FT options are the default choices provided by iNMR 2.4. Scales are referenced according to the “O1” parameter found into the Bruker files. Other treatments are: digital water suppression and polynomial base-line corrections (performed along all dimensions and all lines; the order of the polynomial is 2 along the direct dimension, zero along the indirect ones). In all the examples provided, iNMR over-estimates the baseline to subtract and therefore leaves negative traces. They are trivially hidden (the negative contour levels are not shown), but you may choose to show them. Alternatively, you can either skip the baseline correction or perform a further processing with the console command "noneg()" which cancels all the negative elements of a matrix.
To select the planes for observation, go to the last panel of the Scale dialog (Cmd-G). The f1-f3 are the most informative planes. To swap the x and y axes there is a shortcut that bypasses the dialog: press T (uppercase) on the keyboard. The keys r and t (lowercase) let you move across the slices of the 3D cube.
You will find the phase already corrected but it's not clear, from the examples,
how the corrections were determined. Here's the recipe.
Extract the first plane (create a single horizontal
mark as low as possible, then
press Cmd-E). Repeat the same operation to extract the first row.
Fourier Transform.
Correct the phase (a zero order correction is enough).
Close the extract twice (or Reload the whole data set).
Perform the three FTs (with the hypercomplex
option along the indirect dimensions) and
with minimal zero-filling.
Remember that the number of points along the indirect dimension
is halved because they are phase-sensitive spectra. For example: if you see 48 increments
along the 15-N dimension, they will become 24 points before FT, therefore a size
of 32 does not truncate your data: it's a minimal and effective zero-filling.
Once you have arrived into the frequency domain, select the side containing the f1 and
f3 dimensions. Browse through the planes until you find the plane with the maximum number of
peaks. Now correct the phase along both directions, if needed. First Order corrections may
be necessary.
When done, transpose
the cube to show the f2-f3 planes and check the phase. Correct it, if required.
When you have arrived at the best correction parameters, reload the FID and reprocess it.
This time uncheck the hyper-phase option and zero-fill as much as you like.
Different pulse programs and different instruments will require different processing parameters. We'll try, if possible, to add another sets of examples. You can contribute. Even the present examples are not guaranteed to be correct! The 1D and 2D components of iNMR have been well tested by hundreds of customers. The 3D part has been very little used and may contain some defects. Hopefully, this set of spectra can encourage the use in future.
written by Giuseppe Balacco in 2008