547. NMR on Debian Jessie: gSim

Note: the gsim deb needs glibc 2.14, while wheezy has version 2.13. See here for how to deal with glibc > 2.14 on wheezy: http://verahill.blogspot.com.au/2014/03/562-pulling-in-glibc-214-from-testing.html

gSim is a free program (doesn't appear to be open source -- I can't find the source anyway) for processing 1D and 2D nmr spectra. I don't have much to say about it other than that it seems to provide all the things I require of an NMR processing program, including line fitting (deconvolution).

One neat extra is that gsim has a terminal-like window at the bottom similar to xwinnmr/topspin so that you can control the processing completely via the keyboard. 

gSim can be downloaded from http://sourceforge.net/projects/gsim/

 

installation via gdebi

splash screen

can read bruker files

fid

overview of processing options. I had to select bruker to correct the fid before doing ft

zooming is a bit awkward, but can be done using the mouse

I had some issue with deconvolution

awkwardly it uses ppm for the width too if the x axis is in ppm

you can always switch to hz though

gsim also reads the acqu/s files

It can output the spectrum to eps in case you're too lazy to work in gnuplot

546. NMR on Debian Wheezy: ACD/LABS NMR under Wine

I'm currently exploring options for processing NMR data on linux (see e.g. here for nmrnotebook). There are four categories of programs:
* proprietary/for-cost running natively on linux

* proprietary/non-open source but gratis running natively on linux
* gratis and open source running natively on linux

* windows programs that happen to run ok in wine

ACD/LABS belongs to the last category, and as such is not an ideal solution. However, at this point I'm willing to try just about anything.

So yes, this relies on you having wine installed, but sometimes we need to be pragmatic like Torvalds rather than dogmatic like Stallman (the world needs both of them).

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Either way:

First register at http://www.acdlabs.com/account/register.php?redirect=/account/logout.php

Then download

 

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Installation:

Install by running

wine ~/Downloads/nmrproc_academia12.exe

Go through the installation steps:

 

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Running the software

For most of the steps below there's little need to provide a commentary:

I could only get it to fit by hitting 'Auto'

However, 'Auto' did respect my choice of function e.g. lorentzian vs mixed.

You can export the data as simple ascii files

 

In conclusion I must say that I'm fairly happy with this piece of software. I haven't used it for production purposes, so I can't vouch for it spitting out reliable data though. It's definitely worth exploring though.

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.

License
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..

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Installation

There are two files to download: NMRnotebook.sh and NNBMACROS.zip

Run NMRnotebook.sh

sh NMRnotebook.sh

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:

~/NMRnotebook/NMRnotebook

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/NNBMACROS.zip ~/work/nnbmacros
cd ~/work/nnbmacros
unzip NNBMACROS.zip

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

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Overview

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.