biglogo.gif (GIF Image, 800x418 pixels) http://matnmr.sourceforge.net/pics/biglogo.gif
1 of 1 12/06/06 05:47 PM
matNMR Manual Page: Navigation file:///home3/jabe/matlab/matNMRSourceCode/WebPages/manual/navigate...
1 of 3 02/28/07 05:48 PM
To go to the matNMR project page at source forge:
To go to the source forge homepage:
To go back to the matNMR page:
Search the manual pages directly
1 How to read this manual ?
1.1 Which parts should I read?
2 Installing matNMR
2.1 Installing matNMR
2.1.1 UNIX
2.1.2 MS Windows/MAC
2.2 Setting up matNMR (Options)
2.2.1 General options
2.2.2 Colour scheme settings
2.2.3 Screen settings
2.2.4 Font list
2.2.5 Line properties
2.2.6 Text properties
3 MATLAB and matNMR
3.1 MatNMR and the workspace
3.2 Input expressions
3.3 Important variables
3.4 Where is the NMR?
3.5 matNMR format for spectra
3.6 GUI and MATLAB
3.7 Memory usage
3.8 MATLAB and WYSIWYG
4 Processing in matNMR
4.1 Processing spectra with matNMR
4.2 1D, 2D and 3D mode
4.3 Using the processing history
4.4 Using macro's
4.5 Multi-window matNMR
4.6 Using short-keys
4.7 Apodizing FID's
4.8 Fourier transform
4.9 Phasing spectra
matNMR Manual Page: Navigation file:///home3/jabe/matlab/matNMRSourceCode/WebPages/manual/navigate...
2 of 3 02/28/07 05:48 PM
4.10 Baseline correction
5 The main window
5.1 General appearance
5.2 The menubar
5.2.1 Stop matNMR
5.2.2 Files
5.2.3 1D Processing
5.2.4 2D Processing
5.2.5 Plot manipulations
5.2.6 History/Macro
5.2.7 Create Output
5.2.8 Options
5.2.9 Help
5.2.10 Clear functions
5.3 Fitting of CSA tensors (MAS)
5.3.1 General appearance
5.3.2 Buttons
5.3.3 Menubar
5.4 Fitting of CSA tensors (Static)
5.4.1 General appearance
5.4.2 Buttons
5.4.3 Menubar
5.5 Fitting of Diffusion Curves
5.5.1 General appearance
5.5.2 Buttons
5.5.3 Menubar
5.6 Peak Deconvolution
5.6.1 General appearance
5.6.2 Buttons
5.6.3 Menubar
5.7 Fitting of Quadrupolar tensors
5.7.1 General appearance
5.7.2 Buttons
5.7.3 Menubar
5.8 Fitting of Relaxation Curves
5.8.1 General appearance
5.8.2 Buttons
5.8.3 Menubar
6 The 2D/3D Viewer
6.1 General appearance
6.2 The panel window
6.2.1 Contours
6.2.2 Mesh 3D
6.2.3 Stack 3D
6.2.4 Raster 2D
6.2.5 Tools
6.3 The menubar
6.3.1 Stop 2D/3D Viewer
6.3.2 Plot manipulations
6.3.3 History/Macro
6.3.4 Printing Menu
6.3.5 Copy figure
6.3.6 Options
6.3.7 Help
6.3.8 Clear functions
7 Producing output
7.1 Printing menu
7.2 Saving figures to disk
7.3 Using the Clipboard
matNMR Manual Page: Navigation file:///home3/jabe/matlab/matNMRSourceCode/WebPages/manual/navigate...
3 of 3 02/28/07 05:48 PM
8 Scr
i
pt-
b
ase
d
process
i
ng
Search the manual pages directly
matNMR Manual Page: Introduction file:///home3/jabe/matlab/matNMRSourceCode/WebPages/manual/ManualInt...
1 of 1 02/28/07 05:28 PM
Chapter 1 - How to read this manual ?
This manual was first written for matNMR 2.6 (October 2000) and describes all features and concept of it. Subsequent releases have been incorporated into the manual. This
means that the version that can be found on the website belongs to the latest release of matNMR. I am well aware that this manual is quite limited. It does for example not have
an index and it doesn't allow searching through it. If anyone feels up to improving it, then please do so and send me the result!
The manual is divided in several chapters focussed around some subjects. For all features the actions required to perform it and also the implementation are described (in
short). The description of the implementation shall contain more information about what is done to a spectrum and how matNMR works. In most cases there will be no
explanation of standard MATLAB commands or features; the user is referred to the MATLAB documentation then. Also no explanations will be given for typical NMR operations as
these can be found relatively easy in the NMR literature.
In many occasions there will be spoken of "The main window" and the "2D/3D Viewer". These are the two main windows in matNMR. The first is used for processing while the
second is used mainly for displaying and analysis. They can be started independently from the MATLAB command line by typing "nmr" or "nmr2d" respectively. More
information about these windows is given in chapter 5, "The main window" and chapter 6, "The 2D/3D Viewer"
In the manual there will be made no clear distinction between an FID, a spectrum or a matrix. MATLAB does not care about the NMR behind a spectrum as it only knows
matrices and vectors (for more information see paragraph 3.4, "Where is the NMR?"). Therefore whenever it says "FID" or "spectrum" in this manual it could just as well say
"matrix" because in the end they're all the same thing.
1.1 Which parts of this manual should I definitely read ?
MatNMR can in principle be used as an independent processing program, just like any other package, making knowledge of MATLAB not really necessary. To use all its
features to the fullest however one needs to know some things about it. These things are explained in chapter 3, "matNMR and MATLAB". There the interaction of matNMR and
MATLAB is described in some detail. Even when you don't intend to do fancy stuff however I strongly advise you to read this chapter!
Also I advise you to read Chapter 4, "Processing in matNMR". This explains how processing in matNMR is thought to be done. Also things like using the processing history and
macro's effectively are explained in more detail here.
The installation of matNMR is explained in chapter 2, "Installing matNMR". How to configure matNMR to your personal likings is described in paragraph 2.2, "Setting up
matNMR (options)".
Finally for people who don't want to use the matNMR user interface Chapter 8 , "Offline Processing with matNMR" explains how to use the processing capabilities in
user-defined scripts.
