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Getting Stated with NUTS

Proccessing Bruker and WINNMR FILES

Sample Spectra

Notes on Nuts (Updated Feb. 3, 1999)

To download these notes in Acrobat format, click here!

Dr. Rob Schurko

The following is a very basic introduction to the NUTS NMR processing package, which should get you started in processing NMR data from the Chemagnetics NMR spectrometers, and some other data formats.

Outline

1. Transferring data from the CMX computers to PC's

2. Data translation - NUTS is capable of reading NMR files from a variety of software packages, though there are a few tricks and errors that should be addressed.

3. Basic processing and operations, including EM, FT, zero-fillings, phasing, left-shifting, zooming, etc.

4. Baseline correction routines

5. Dual display of spectra, and file algebra

6. Display of multiple plots - problems and solutions

7. Document ready spectra - how to incorporate spectra into your documents

8. WinSOLIDS and NUTS - how to make two very different programs communicate

1. Transferring data

The simplest way to get the data off of the CMX machines is by directly ftping the files to the appropriate directory on the PC. The program WS-FTP is useful in this respect.

Both Chemagnetics and Bruker spectrometers store NMR data in a directory format, meaning that if you acquire a spectrum and call it "spectrum1", a directory named spectrum1 is written to disk which contains all of the relevant data, acquisition parameters, processing parameters, etc. Thus, the whole directory must be transferred and left intact on the PC.

NUTS on the other hand, saves all of the data in a single file. Temporary NUTS files have a dollar sign ($) at the front of the filename, and should be saved in a permanent place in a directory that belongs to you. Keep things neat, not like the mess downstairs on the CMX computers.

2. Data translation

A. Chemagnetics

Chemagnetics datasets have the following files within the directory structure. You should learn why each of these files is needed by the software!

acq acq2 data proc proc_setup 1pulse.acq setup setup_setup

The important file here is the data file, which is a binary file containing the real and imaginary points of the FID.

There are several options for opening files, located under the File menu. Once you get use to using NUTS, you may prefer using the two-letter command series that is available (vide infra). Open (GA) is useful for opening NUTS files, and will attempt to open non-NUTS files. If you are importing files from other spectrometer formats, you should use Import file (IM), and this will automatically detect the file type.

So, for a Chemagnetics file, type IM, change into the directory of your file, and double-click on data. The FID will shortly display on your screen. You are now ready to begin processing.

B. Bruker and WINNMR

Bruker and the associated processing software, WINNMR, store the data in a similar manner to Chemagnetics, however, the data file is broken into two separate real and imaginary files. In most cases, you can simply click on the "reals file", which is denoted by 1r or filename.1r.

The current version of NUTS has difficulty reading WINNMR files, because it is looking for an outdated file with the extension "DIS", which comes from old Bruker DISNMR software. I have alerted them to this problem, and they are currently rectifying it for the next version.

If a DIS file is not present, copy filename.aqs to filename.dis, and make the following adjustments:

Change:
SFO1 to SFREQ
SW_h to SPWIDTH
TD to TDSIZE
and double the size of TD for TDSIZE (e.g., TD = 2K, then TDSIZE = 4K).

If the DIS file is present, just make the above adjustments.

3. Basic processing and operations

A. Processing conditions

From the menu, select Processing, then Conditions. From here, you can set the appropriate amount of line broadening (LB), as well as some other parameters.

B. Zero Filling

Just type ZF for each zero fill (doubles the number of points).

C. Exponential Multiplication

Just type EM, or click Process, Window functions, Exponential Mult.

D. Left-Shifting

For some reason, you can only shift one point at a time, by typing LS (or using the menu under Edit). If you need a load of left shifts, this is easily circumvented by using the handy linking option provided in this package (see below). You can also right-shift (RS).

E. Links

Links are accessed by typing LI, or selecting them from the Process menu. These are 10 quick little commands that are built up from strings of two-letter commands. So, if link 0 is: BC EM FT PH, this baseline corrects the FID, applies EM, Fourier transforms, followed by phasing controlled by the mouse. To activate link 3, for example, type A3. If you need a link to perform multiple LS operations, just edit the appropriate link.

To permanently make links, you must edit the NUTS.INI file, which configures NUTS. Be careful, and record any changes you make in the correction area of this file. You don't want to ruin links or anything else that people have set up in this file.

F. Fourier Transform

If you haven't guessed yet, just type FT, or use the menus (which slow things down!!!!).

G. Spectral Reverse

***N.B. There seems to be a curiosity with some Chemagnetics data files and how they are translated. After you FT your spectrum, you may noticed that it appears "reversed" (i.e., a mirror image in terms of chemical shifts, etc.). Just type SR, and the problem will be rectified, with all of the correct chemical shifts. The people at ACORN NMR are currently looking into this.

H. Cursor and Zooming

When the left mouse-button is depressed, you can move a crosshatch around the screen, and are provided with information on the points, Hz, ppm and intensity.

If you double click, you enter zoom mode. Here, you can highlight a region of the spectrum and zoom in on it. To return to the full screen, double-click the right mouse button.

To exit various modes in NUTS, just hit enter, until you see Base level at the bottom of the screen.

I. Phasing (Using the Mouse)

There are a variety of options for phasing, I think that this one is the best.

First, hold down the left mouse button (to get the cursor) and move it to where you want to set the zeroth-order phase pivot. Still holding onto the left button, press P. The pivot is now set.

Type PH to enter mouse phasing. The left button is zeroth order, the right button is first order. Hit enter when done.

J. Vertical Offset

By typing DC, one enters a mode in which the vertical positioning of the spectrum can be altered. Just use the sidebar to alter the vertical positioning, and press Enter when done, so as to exit this mode.

That's it for basic stuff. There are plenty of things for you to experiment with.

4. Baseline Corrections

There are two methods available: a polynomial fit (recommended) and a spline-fitting, line-straightening routine (not recommended). Stay away from the latter unless absolutely necessary, as it will change the relative intensities of peaks etc. The former method will be dealt with here.

With the processed spectrum on the screen, and already phased, type FB to fit the baseline. You will see a series of red bars come up on the screen where NUTS suspects that there is minimal signal intensity. By clicking on a white area of the screen, you can select that point for fitting by the polynomial routine. Clicking on a red area shuts off that point.

When you are in the fit baseline mode, you can type L (or use the menu) to perform a least squares fit, and P to display the fit polynomial. Hitting Enter will exit this mode and apply the correction.

For extremely distorted spectra, you may choose to baseline correct only a portion of the spectrum. This is accomplished by zooming in, and using the FB routine described above.

5. Dual display of spectra

This is useful for displaying two spectra of the same size, and performing file algebra on the two spectra (i.e. difference spectra, summing of spinning sidebands, etc.).

  • Use GA to select your first file.
  • Type AL (or click this under Tools, Add/Subtract Routine) to load the add/subtract buffer.
  • Open the second file (it may also just be the first file, if you are summing spinning sidebands).
  • Type AS to enter the add/subtract routine (or click, as described above)

The two spectra will be displayed on the screen. You can change the multiplier of the spectrum in the buffer to adjust intensity by pressing M, or the horizontal offset by pressing O. All the options are displayed in the new menu at the top of the screen, including difference spectra and addition of spectra.

To exit, simply press Enter.

6. Display of multiple plots

There are two ways to go about doing this:

  • Create a 2D file which contains an unlimited number of files
  • Use the buffer mode

Method i: "2D file"

The files you used must be named such that they are sequential, e.g.:

filename.001, filename.002, filename.003, etc.

There is no limit to the number of files that can be stacked, but they must all be the same size.

Create the link: GA SC IN (you can read about these commands in the online help)

and run it.

Input the name of the first NMR file (001), and then you will be prompted for the filename of the 2D file. All of the files will be inserted here, and you can then open this file and play with it.

Processing the 2D file is straightforward in most cases - you probably want a stack plot, so type SP, and watch what happens. You can add whitewash effects, tilt the spectrum, etc. Adjusting relative intensities is a bit more tricky. This will be updated in the near future.

Method ii: "Buffer mode"

Use GA to open the first file. Type BU (not in the menus) to enter buffer mode. Using the menus, you can Transfer the file to any of the buffers. The buffers are displayed from 0 to 10, from bottom to top. The intensities and vertical positioning of the spectra can be altered using the menus. The only disadvantage of using buffer mode is that you cannot plot the spectra on an angle as in Method i above. You can however, use the nice cut-and-paste utilities to make some pretty great pictures (see section 7, below).

7. Document ready spectra

One of the great things about this software is that you can paste directly into programs like Wordperfect Presentations, Powerpoint, and any number of Windows programs. The spectral positions, sizes, colours, etc. can be manipulated in the graphics program quite easily.

There are a number of choices for doing this, and the best method is to find what works with the software you are using. All of the options are located under the Edit menu. You can copy to the clipboard for direct pasting, or you can copy to files. The best spectra are produced (it seems) with metafiles, though bitmaps can be of some use as well.

Simply: copy to the clipboard, and paste into your choice of picture making software. Then, edit away and make beautiful pictures. I do not know if this works with Canvas. Someone let me know. Anyhow, no more postscript, etc.

8. WinSOLIDS and NUTS

WinSOLIDS is an incredible program written by Dr. Klaus Eichele, while he was in Dr. Rod Wasylishen's group at Dalhousie. The program is capable of a variety of solid-state NMR simulations, and can be very useful provided you know what you are doing. However, WinSOLIDS only reads and saves certain kinds of files. WinSOLIDS is primarily written for use with WINNMR and Bruker spectrometers, but thanks to NUTS we can now use it for spectral simulations.

Reading files

Since we do not use Bruker spectrometers, the best format for reading your experimental spectra into NUTS (for comparison with simulated spectra) is using Klaus' SOLIDS.DAT format. It is basically an ASCII file containing the real intensities of the spectrum, with a five line header. The format is:

SI size of the file
SF spectral frequency
SW/SI spectral width (F1 - F2)/SI
F1 high frequency limit
F2 low frequency limit
list of real intensities

You can make such files by exporting your processed data to an ASCII file. Under the File menu, choose Export Data, and Real Data Only ASC Export. Then, edit the file using Notepad or DOS, and add the five lines above onto the file. Give the file the extension "dat" i.e., filename.dat.

Writing files

Currently, WinSOLIDS saves files in WINNMR format, outputting files with the extensions 1r (real), 1i (imaginary), aqs (acquisition parameters), fqs (contains the spectral referencing) and dis (old DISNMR format). It turns out that the 1r and DIS files are the most important, at least for NUTS. So, simply save the spectra in WSOLIDS, usually as something like:

001001.1r (which means JOB 1 PROCESS 1. REAL, in Bruker/WINNMR jargon).

Now, back to NUTS

NUTS, as mentioned, can read in WINNMR files. This is useful now if you want to make a nice picture comparing experimental and simulated spectra. All you have to do is:

  • Edit the DIS file as outlined in section 2.B. of this document
  • Read it into NUTS (you can use dual display, etc.).

Conclusions

I sincerely hope that you find the NUTS software very helpful, since it allows you to process your spectra and prepare them for publications, posters, and yes, even theses, in a quick and straightforward manner. If you have any difficulties with using the software, please let me know, and we can see if a solution to your problems is possible!

Thanks a lot,

Rob