Processing NMR data-set, is just issuing a series of correct commands along with correct parameters. You will find starting from here a list of commands, by topics. A list of commands by alphabetic order can be found on an other part of the manual.
Commands are presented here ordered by functionality, and oriented toward the command level, in contrast with the previous chapter oriented toward the user interface. Extending the user interface can be simply done by learning and using these commands, and the macro language.
As you have seen if you have been through the primer, Gifa is an interactive program : it waits for commands from the user. Some commands have parameters some don't; some commands may even have a variable number of parameters depending on some context value (it is a so-called context-dependent grammar).
There are two kinds of commands in Gifa : regular commands which actually execute some action (such as FT for Fourier transform), the others are commands which may execute an action but will also change the value of internal parameters of the program (such as LB for line broadening). Such commands will be called contexts.
For instance HELP is a regular command, but DISP1D is a context which handles the parameter describing the state of the graphic 1D window. A good example of this distinction is given by the context LB which defines the default value used for exponential broadening, as compared to the related EM command which actually apply this exponential broadening to the current data-set.
Most of the behaviour of the program depends on these internal parameters (contexts). Another example of a context is DIM which describes whether we are working with 1D 2D or 3D data-sets .
For instance, type :
Gifa> DIM 1 ; switches to 1D NMR
Gifa> size ; lists basic parameters
Gifa> DIM 2 ; switches to 2D NMR
Gifa> size ; lists basic parameters
( characters following the semicolon are comments )
The effect of the command size (which lists the basic parameters of the current data-set) depends on the state of the context DIM.
Most contexts have associated Gifa variables which permits to evaluate its value during macro execution. See the chapter on variables for details.
Commands can be issued alone, in which case, the command will prompt you for all the values it needs, proposing default ones. Default values may be kept by hitting the <enter> key, or may be changed by typing new ones. You can also type the parameters on the same line than the command; the effect is then immediate. When using in-line entry, the different item will be separated by blanks.
Several commands can even be typed on a single line, separated with a blank. For instance to get back to 2D display mode, you could either type :
Gifa> DIM 2
Gifa> size
or, on a single line :
Gifa> DIM 2 size
The effect would be the same. The only difference is that the graphic is only refreshed at the end of the command line; this permits to link together related commands, without slowing down the process by useless display (irrelevant in the present example).
Most commands and macro promt for parameters. There are general rules for parameter entering which I will try to descibe here.
zoom 1 10i 10i 200i 300i
zoom 1 8.3p 8.3p 7.5p 6.5p
zoom 1 6000h 6000h 4500h 4000h
or even mixed :
zoom 1 10 10i 7.5p 4000h
actually might defined the same zoom window (values are given as an example)
The standard way of working on an NMR spectra with Gifa is to hold everything in memory. This is in contrast with most NMR programs that process data on disk files, and permitted by a clever memory management.
So, to process a data-set with Gifa, you generally load it in memory, do most of your processing, plot it, and optionally store the processed data on a file for later processing. This permits a very fast processing on small every-day data-sets. When a larger data-set necessitates to work on a file, then a set of specialised commands permits to use all the regular commands on file.
Gifa presents several buffers to store the data. Three working buffers are available for respectively 1D, 2D and 3D. These 3 buffers are independent for regular processing. The buffer on which you are working depends on the value of the context DIM which takes the value 1, 2 or 3.
All the commands refers to the current buffer (as selected by DIM). Depending on the value of DIM, some commands may ask for a varying number of parameters ( 1 per dimensions ) others may ask for direction, in which case the direction is selected with the syntax Fx. In 2D : F2 for the acquisition dimension, F1 for the other and F12 for both. In 3D : F3 for the acquisition dimension, F1 for the slowest dimension, F2 for the intermediate dimension, and F12, F13, F23 and F123 for combinations. When a command requires a parameter for each dimension, F1 parameters will be entered first, then F2 and finally F3 (if in 3D), this rule is general, with the exception of graphical commands which will ask for X and then Y parameters.