Processing Data with NUTs for PC/MAC

This was supposed to be the fourth of four emails related to working with NMR data on a PC/Mac computer rather than print to paper then scan the document; however, I have broken this one into 2 different emails. These two are related to working with the data (so actually processing/displaying the data) on your PC/Mac. There are 2 distinct ways to accomplish this:
1) Use an NMR processing program than runs on PCs or Macs
2) Run the NMR processing program (VNMR) on the Sun (or SGI) workstation, but display the program on your PC/Mac

Thus, this email will be related to the first of those 2, using an NMR processing program on a PC/Mac.

We have a site license for a program called NUTs, from Acorn NMR which runs of PCs or OS 9 Macs (or Classic for OS X).

The primary advantage of using NUTs is the data is on your computer.

The primary disadvantages are:
1) You have to learn another NMR software program, but basic NUTs is pretty easy to use.

2) NUTs is an inferior program to VNMR despite VNMR's quirks. Simple 1D spectra are ok, but using NUTs for 2Ds is difficult.

3) When you acquire any NMR spectrum, there are processing parameters that are preset for you, you now have to set these yourself or go without adjusting the processing parameters; this is not much of a problem for a 1D 1H spectrum, you might hurt your signal-to-noise or resolution slightly, but it would likely be barely noticeable. For 13C 1D and 1D NOE, your signal-to-noise would be hurt enough that it would likely be noticeable. Thus, you should become somewhat familiar with zero-filling, exponential multiply, gaussian multiply, etc.


Step 1.
Download the NMR processing program, NUTs, for PC.

You will need 2 files; email me and I will send them as an attachment; you need to say PC or Mac as the files are OS dependent.

Next, there are 3 steps you need to follow:

1. Download and install win_nuts.exe from the web site (http://www.acornnmr.com/win_nuts.htm). This is a self-extracting ZIP file,so you just execute it. It requires a password, which I will send you with the email.

2. Save the attached files (the license and the sam.dll) in the NUTS folder. Be sure the file names are not changed when you save them. You cannot open these files. Nuts will look for them and read information it needs from them when it isstarted. You will know that this worked correctly, because your name shouldbe on the initial screen. If not, read the troubleshooting information at http://www.acornnmr.com/installation.htm. If problems persist, let me know.

3. [Not necessary for Win2K or XP]
If this is the first time you have installed NUTS, you will need to execute the file called hhupd.exe, which installs systems files needed to display the NUTS Help files. (See details at http://www.acornnmr.com/NutsHelp/help_files.htm )


For Mac:
Download NMR processing program NUTs for Mac.

You will need 2 files; email me and I will send them as an attachment; you need to say PC or Mac as the files are OS dependent.

First, download and install MacNUTS Installer.sea.bin from the web site (http://www.acornnmr.com/macnuts.htm). This is a self-extracting Stuff-It archive, so you just double-click to execute it, then run the Installer. Read the notes displayed at the beginning of the installation process, because that explains what files are installed.

Then just save the attached files in the MacNUTS folder. Be sure the file names are not changed when you save them. You cannot open these files. Nuts will look for them and read information it needs from them when it is
started. You will know that this worked correctly, because your name should be on the initial screen. If not, let me know.

You should download the version that says:
Download MacNUTS installer for PowerPC
as the other versions are for ancient Macs- pre-PowerPC.

There does not seem to be any version that runs directly on OS X, this version will run on Classic Environment (OS 9 like on an OS X Mac)

Step 2. Run NUTs software.

Mac and PC NUTs seem to be nearly identical, so these directions should hold for either one:

1. Import data. Use import under File menu, find your data; remember that Varian data is actually in a directory (or folder) something.fid then find the fid within that directory. The NUTs program should understand that the data is from a Varian and translate it.

2. Process data.

Below are a few useful functions on how to run NUTs software. For more information, there is a Help menu. In addition, most standard functions are accessible from the top menus. Also, there is more help on the NUTs website: http://www.acornnmr.com/NutsHelp/index.html

First read data, then Fourier transform data:

ft = Fourier Transform
ap = Auto Phase

Middle mouse adjusts vertical scale. There are also scroll bars on side to scroll up/down or right/left across spectrum. And, the command mf does the equivalent of vsadj.

To zoom in on part of spectrum, you can Double click left button and drag; dragging highlights, then Ctrl e will zoom. Ctrl f will take you to full spectrum. f will allow you to manually set frequency range.

If you are in the normal mode, type:
id
to enter integral display

In integral display, type:
b
to allow you to fix level/tilt with mouse button

To set integrals, click once to get cursor, then click again on either side of the resonance to integrate.

To set value of an integral, click once to get red cursor, position it over peak and type:
v
then establish value of integral of that peak.

Hitting return should take you back to main level of program; to toggle between showing/not showing integrals now, type:
Ctrl i

That covers the easy standard functions.

In addition it is easy to use Weighting Functions:
Signal-to-noise enhancement: em = exponential mulitply, gm = Gaussian multiply
Resolution enhancement (maybe): tf

Zero Fill: zf

Baseline Correction: bc

Note that weighting functions and zero fill should be done before the Fourier transform, baseline correction can be done afterwards.