NUTS Frequently Asked Questions
Q. Is there a Linux version of NUTS?
A. No. However, customers have reported that the Windows version of NUTS runs well on Linux under Windows emulators WINE and Cross Office.
Q. There is a glitch in the center of my spectrum. How can I get rid of it?
A. A center glitch arises if there is a DC offset between the 2 channels. Both real and imaginary parts of the FID should decay to zero by the end of the acquisition, but sometimes that "zero" level is not truly zero, and the offset may not be the same for both channels. A BC command, issued before the FT, is used to adjust the DC level of each channel to real zero, and will eliminate the center glitch. See example.
There is an exception to this – if the FID has NOT decayed to zero (e.g., truncated 2D data), applying a BC may create a DC offset, and cause a glitch to appear. See details.
Q. I have a spectrum with a folded peak. Is there a way to correct this with NUTS?
A. Yes, provided a few conditions are met. The RD command, which performs cyclic rotation, can be used to "fix" a spectrum with folded peaks. See details.
Q. How can I most easily distribute spectra to NMR facility customers?
A. Data can be emailed or posted for download. The customer’s computer is easily configured so that (s)he can just click on the file name or icon, which launches NUTS, loads the data and displays it according to the customer’s preferences. See details.
Q. How can I get the best quality image pasted into a report?
A. Very good images can be created from NUTS, but accomplishing this requires an understanding of how copying via the clipboard works. See Copying for an explanation.
Q. How do I put my own logo in place of the acorn on my screen and plots?
A. Edit the nuts.ini file. To remove the acorn, "comment out" (put a semicolon at the beginning of the line) the line that consists of MetaObjectFile. To replace the acorn with your own logo, put the file name for your logo in place of acorn.emf. (Your logo must be a metafile.) The purpose for displaying the acorn was to illustrate how users can insert a logo of their choice. Note that Nuts must be restarted for this change to take effect. To remove the logo while in Nuts, enter the MO (metaobjects) subroutine and use D to delete the image.
Q. On some files, when I do Automatic Integration, numeric values are not displayed. Why not?
A. When AI is executed, the smallest integral found is set to one. If your baseline is poor, this integral can have a negative value, so Nuts defaults to setting it to zero, and no labels are displayed. Try baseline correcting, then redo AI.
Q. I am having trouble with the integral values. I dont see any values associated with the integrals either at the top of the screen or under the integrals themselves.
A. As soon as you start defining integral regions for different peaks, you can assign a convenient value to a selected integral. Click the mouse button once to get a red vertical cursor. Place that cursor so that it is on top of the chosen integral. Type V (for value) which brings up a box in which you can enter a value. Until you do this, no values are defined, so none are displayed. The scaling factor you have now set stays the same until explicitly changed by you, regardless of the display scale of the spectrum or the integral trace, even if you leave the integration routine and re-enter.
See Integration for illustration of how to do this.
Q. My data was acquired with block averaging. Can NUTS sum the files automatically?
A. Yes, as long as the files have sequentially numbered file extensions (file.001, file.002…) Create and execute a Link which consists of commands:
GA AS AL IN
See Add/Subtract for details.
Q. The spectrum looks OK on the screen, but when I print, the axis and integrals are scrunched into the first 2 inches of the left side of the plot.
A. This was a problem with some printer drivers. Changes were made to NUTS as of May, 2005, to work around the problem.
Q. After doing a fit in the line fit subroutine, I need to report the error for the fit to the actual data. There is an error value printed on the screen. What is the meaning of this error value?
A. The error reported during LF Simplex fit is calculated as described below. It has no statistical meaning but was developed empirically to perform the best guide for the Simplex routine.
error = 100.0 times (difference between actual points and calculated points, squared) divided by (square of all points)
See Line Fit routine for illustration of how to use this subroutine.
Q. My spectrum after FT appears to be backwards. What is wrong?
A. This is easily fixed with the SR (Spectrum Reverse) command. Why it happens is more involved. For GE Omega data, this can result from the way the frequencies are generated in the spectrometer. For example, proton spectra may be correct, but carbon spectra are reversed. There is no way for Nuts to know which is correct, so this must be corrected manually. At one time, it appeared that importing of Varian Unix data resulted in reversed spectra, which has since been corrected. You can configure your nuts.ini file to perform this correction automatically when data is imported, but be advised that this will then be done on every data set. If you process data from different sources, this may not be advisable.
Q. My Bruker data has huge quadrature images, even though the spectrum looks OK on the spectrometer.
This can result from either of 2 sources, both related to the fact that Bruker does "quadrature" detection in a strange way, which they call "sequential" acquisition. This means that they use a single A-to-D converter, and digitize the data at twice the normal rate, alternately placing points into the A and B channels. Therefore, the data does not exist as true quadrature pairs because the real point and its corresponding imaginary point were not acquired at the same time. This necessitates a special type of FT. Nuts should correctly identify Bruker sequential data, and apply the "Bruker" transform when the FT command is executed. If your data type is incorrectly identified, executing an FT command will use the wrong type of FT, and cause large images. Check the Data Type parameter (View menu/ Spectral Parameters) to be sure it is correct. Bruker sequential data is identified as "TPPI", simultaneous data is identified as "Complex", non-quadrature data is identified as "Real".
These quad images can also result from swapping the real and imaginary channels, which can happen when the data is transferred to the PC. In this case, executing an RI command on the FID will swap the 2 halves of the data, and subsequent FT should produce a correct spectrum.
See description of Bruker artifacts for illustration.
Q. How do I process Bruker digitally filtered data?
A. Bruker does some pre-processing before saving the data, so that the FID looks strange. The initial points are zero, then build up to the beginning of the FID around 60-70 pts from the beginning. To process this data, you must first do a circular left shift so that the top of the FID is at time=0. The command is RD. Nuts should correctly calculate the number of points to shift. See Bruker digitally filtered data for illustration.
Q. How do I display a chemical structure on my plot?
A. This is done in a subroutine called MO (stands for Meta Objects). This routine is also one way to create inset plots. The Windows version now allows you to place a standard, placeable or enhanced Windows metafile onto the screen, either from a file or from the clipboard. This can be a chemical structure, a logo or other graphical object. (Note that Win 3.11 does not support enhanced metafiles.)
The Mac version uses PICT files instead of Windows metafiles. You can also copy a PICT file into the clipboard from some other application and paste it into Nuts. This works best if you make the object fill the screen before you copy. You can also import a PICT file from a file. However, this does not print properly. The size of the object when printed is much smaller than on the screen. This seems to be because PICT files don’t keep track of the size as it relates to printer resolution. So, at this point, using the clipboard seems to be the better alternative.
More than one object can be displayed on the screen. The program keeps track of them in a linked list. Each object can be moved and re-sized using the mouse. To select which object to operate on, you move through the list, forward or backward, until the desired object is indicated with a box with handles for re-sizing (see below for command list).
In the Windows version, there is also the option of defining one or more graphical objects in the nuts.ini file which will be displayed on the screen automatically. (This does not currently work on the Mac.) This is demonstrated in the Windows version by the display of the acorn in the upper left corner of the screen. This can be removed by editing the nuts.ini file or, while Nuts is running, by deleting it from within the MO subroutine.
The MO subroutine does not display menus, but instead has a "helper box" which has buttons for each operation. The buttons are labeled with the corresponding keyboard command. The helper box can be toggled on and off from the Help menu at the base level of the program.
The MO subcommands are:
- A to add the currently displayed region as an inset plot
C to paste the contents of the clipboard
I to import a graphical object from a file
D to delete the selected object
N to move to the Next object in the list
R to move to the previous object in the list
Shift-F1 brings up Help for the MO subroutine
Enter exits the subroutine
- See Meta Objects for illustration.
Q. How do I do a stacked plot of a series of 1D files (such as kinetics data)?
A. If the data exist as separate 1D files, they must be packed into a NUTS 2D file, which can be done with the following Link, assuming the files have sequential file extensions:
GA SC IN
When this is run, Nuts will prompt for the file to read (the first of the 1D files) and for a name for the 2D file to be created.
(For Varian arrayed data, the data is already a 2D file after importing into Nuts.)
Then open the 2D file, execute a SS command (Set Scale) and SP to perform the stacked plot. The offsets in both dimensions can be set using O or by selecting Slice Offsets from the Display menu.
See Stacked Plots for illustration.
Q. I want to create a field in my Access database containing the name of an NMR data file, so that clicking on it will launch NUTS and load my spectrum. Can this be done?
A. Yes. Create a field in an Access table as a hyperlink field. In that field, enter the full path and file name of the data file. You must associate the file extension(s) of the NMR data files with NUTS, so that clicking on the file name will launch NUTS. (You can use File Manager, and select File/Associate). Also, the Access .mdb file must reside in the NUTS directory, so that NUTS can find the other files it needs.
Q. I have a heteronuclear 2D data set, and want the labels on the 2 axes to be different (1H and 13C). But the axes always end up labeled the same. How can I do this?
A. Each dimension is labeled with its "acquisition order". Each dimension must have a different acquisition order label. Switch NUTS to the "non-2-letter" command mode (2F), and type acqorder to see what the labels currently are. To change the labels, type acqorder 1 2 3 4 (for example). Now that the different dimensions are labeled differently, you can change the axis labels from the View/Spectral Parameters screen.
Last updated: 6/24/05.