(The examples are done on a Intel Mac, Os X system. Red is my input. Blue is the computers responce. Black is a comment)
In class, we collected 2D COSY data for Ethyl Crotonate in CDCl3. I have recollected this data on an 800 MHz NMR in ISTB1 L2-63.
This is a Varian 800 MHz NMR running vnmrj. The software looks like:
I loaded in a standard COSY sequence and this set nt=16 and d1=20. This is a very long d1 to use.... but I wanted something that is fully relaxed and it was the end of the day and it did not hurt for this to run overnight (11hr). The COSY I ran is on a 10% Ethyl Crotonate sample in a standard 5 mm NMR tube with the following parameters (dg) and pulse sequence (dps):
with ni=128. Then I collected the data (11 hr COSY data acquisition because of the long d1 and nt=16). I saved the data
svf('Ethyl_Crotonate_Std_COSY_d1_21sec')
The data is saved as a directory with the following four files: fid, log, procpar, text. An archived zip file of the orginal Varian (vnmrj) data is provided here: Ethyl_Crotonate_Std_COSY_d1_21sec VARIAN DATA.
Also, the first 32 slices in ASCII format have been saved using writefid and put as an archived zip file: Ethyl_Crotonate_COSY_ACSII_32fids.zip
Now that you know the basics of Matlab for NMR data processing, I want to introduce you to a wonderful Matlab Program written by Doug Wheeler at the U. Wyoming. This program is a graphical user interface (GUI) set of matlab .m files that is EXCELLENT for reading in most types of NMR data and processing this data.
You can go to Doug Wheeler's website to download the latest version. The version I currently use has been achived as a zip file and included here: MatlabNMR.zip
Unzip the file, start Matlab (with intel mac's in PSH530, you still have to use matlab -nojvm) and go to the directory that you unzipped the MatlabNMR program.
Type nmr at the matlab prompt and this should start the GUI . Now go to Files > Read Varian VNMR Data and use the browser to highlight the fid file from the Varian data set:
The example below shows me highlighting the Ethyl Crotonate fid data set on my computer:
Now you can process the data: Process > Process Data
(It knows this is a 2D data set and will do a 2D FFT)
This creates a procdata2d.mat file into the original Varian data directory.
If you want to get the data in your Matlab workspace (currently it exists in the GUI window), go to File > Copy Data to Workspace
There are way way way to many features to this Matlab GUI. I encourage you to explore this GUI (it is excellent). Furthermore, use this GUI and the associated .m files to understand better how to process 2D data in matlab.
VNMR and VNMRj are software packages from Varian that are designed to COLLECT nmr data. It is not nearly as good for PROCESSING and ANALYZING nmr data. Programs like iNMR, MestReC, AcornNMR, MRUI, RMN, Felix, NMRpipe, Sparky, etc. are software packages for processing and analysis. Also, general programs like Matlab, AVS, Octave, Scilab, IDL, Igor, etc are good packages to create your own processing and analysis routines.
Here are a few more data sets using the 10% Ethyl Crotonate, CDCl3 sample: Simple 1H 1D Bloch Decay and a Simple HMBC.
Enjoy!!