Showing posts with label gui. Show all posts
Showing posts with label gui. Show all posts

31 January 2014

545. NMR on Debian Wheezy: NMRNotebook by NMRTec

While it's possible -- even easy -- to write your own scripts for processing NMR data (e.g. here and here) there's still a value in having a GUI handy.

Either way, this entry is about NMRNotebook, which ultimately derives from another gratis program called Gifa which I experimented with in the early 00s. Apparently after Gifa v4 (article), NMRTec developed Gifa v5. After that there seems to have been a split in efforts (not a fork) where NMRTec developed NMRNotebook, and other people involved in Gifa developed NPK. NMRNotebook appears to use NPK as the underlying engine, but provides a nice GUI which is written in tk/tcl, java and python.

Note that Gifa 4 and Gifa 5 are still available for download, but require license files to run. I don't know if it's still possible to get licenses for Gifa. Based on my memory of running Gifa (4?) the interface was quite slick, and it had a terminal at the bottom, similar to xwinnmr.

Either way, NMRNotebook can be downloaded for free from NMRTec for academic users. You will need to register and then get a license, which can be had by following the instructions on their website and sending off an email with your details.

So I did that.

NOTE that the 1D line fitter is not included in the free version  -- it's priced at 1,000 Euro, which sounds a bit insane to me, in particular if you compare with the price of the software (Euro 100 for a student license, 750 for an industry one). Either way, you can write your own fitter in octave in fifteen minutes..


There are two files to download: and


NMRnotebook installer - starting installation... please wait NMRnotebook will be installed in your home directory. Unpacking ... Running post-install script ... done !! To run NMRnotebook, type '~/NMRnotebook/NMRnotebook' to create a shortcut named nnb in your home directory, type 'ln -s ~/NMRnotebook/NMRnotebook ~/nnb' To uninstall simply erase the directory ~/NMRnotebook and ~/.nmrnotebook Some examples can be found in the '~/NMRnotebook/examples' directory Thank you for using NMRnotebook. NMRtec software team
Run nmrnotebook as indicated:

Import the license by going to File/Open and select the nnb file you got via email.

Close the program and start it again.

Unzip the macros by
mkdir ~/work/nnbmacros -p
cp ~/Downloads/ ~/work/nnbmacros
cd ~/work/nnbmacros

To run a macro, select it and run it:
To be able to launch nmrnotebook from GNOME create ~/.local/share/applications/nmrnotebook.desktop
[Desktop Entry] Name=NMRnotebook GenericName=nmrnotebook Comment=Software for processing of NMR data Exec=/home/me/NMRnotebook/NMRnotebook Terminal=false Type=Application Categories=Science Version=0.27

NMRNotebook can open varian, bruker etc. files. Bruker shown here

Window functions, showing EM and interative LB

Several different types of fourier transforms are available

My first spectrum

Zoom works similar to mestrec

Right-clicking brings up a menu that allows you to integrate, label, draw boxes, lines etc.

Normalised integral

NMRnotebook can accept SR values for calibration

Spectrum overview

NMRnotebook only has a few features available, but is sufficient for basic NMR processing. Line-fitting is the most serious omission.
 Overall I find NMRnotebook perfectly adequate for what I would see myself using it for -- simple processing of NMR spectra. Anything more serious and I'd use my own scripts -- but I'd do that anyway in order to be able to trust the data.