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MACRO: Macros are text files holding regular GIFA commands. Loops, tests, controls, input/output and variables are available within macro. Macros are called form the user interface exactly as native commands. Parameters can be passed to macros. Macro are called by typing their name (case sensitive). It is also possible to force for a macro call by prefixing the name with @. Permitting thus to have macros having the same name as native commands. When called, macro files are first searched in a list of directories, held in an internal path context (The GifaPath). By default the path consists in the current working directory (as given by pwd), then in the user macro directory : $HOME/macro, and finally in the global macro directory : /usr/local/gifa/macro. This PATH can be changed with the SETPATH command, and examined with the $GIFAPATH context. All the macros in the standard distribution are in the /usr/local/gifa/macro directory, some other macro can be found on the ftp server.
MAX: Finds the maximum and minimum points of the current data-set. Load the values used by MINIMAX.
MAXDATA: Compare the content of the current buffer with the content of the DATA buffer, and leave in memory the largest of the 2 values. Usefull for projections or symetrisation macros.
MAXENT: MAXENT SI1 { SI2 } Start Maximum Entropy iteration. The user is prompted for the size of the reconstructed image.
MAXENTCONT: Continue Maximum Entropy iteration. All the parameters may be modified before CONTinuing, but the current spectrum as hold in the working buffer should not be modified.
MEDIAN: MEDIAN { y } x index Executes a median filter on the data-set (1D or 2D).a window of x points (or y by x in 2D) is moved along the data set, the point are ordered, and the indexth point is taken as the new point for the data set.
MEMORY: The GIFA program holds all the data in one single large memory buffer. This buffer is used for several purposes, and may be divided into smaller pieces. The size of this buffer is displayed when entering the program, or with the CONFIG command. There is no way to use a larger data-set than this memory size but recompiling. This buffer is used for 1D as well as 2D and 3D operations. In all cases the whole buffer is available. However, when moving back and forth between 1D, 2D or 3D mode, or when using memory intensive commands, only partial regions of the buffers are protected. The size of these protected regions are given with CONFIG command. The idea is that you can eat-up all the available memory for a single data-set if you which, but that certain operations will be forbidden on it. For instance, you can handle a full memory 2D data-set if you do not wish to do 3D. However, when working in 3D, if you zero-fill a 2D plane extracted from the 3D, over the protected area size for 2D, you will destroy a part of the 3D buffer. You will sometime get the question : 'This will overflow the xx buffer, Ok?' when there is any risk of destroying one of the buffer. This question is not asked in macro execution, where you are supposed to know what you are doing. See documentation for a more detailed description of the memory set-up.
MESSAGE: message text This command ermits to build interactive macros. If no argument is present on the calling line when MESSAGE is executed, the text will be issued to the user when the next data entry will be needed; if an argument is present, nothing will happend. If the macro is called from a menu button, then the text will appear in the data entry dialog box.
METH: METH 0/1/2 When set to 0, indicates that the current build-up curve is taken from 2 simple hydrogens, when set to 1, indicates that there is 1 methyle group, when set to 2, 2 methyle groups. Used by DIST
MINDATA: Compare the content of the current buffer with the content of the DATA buffer, and leave in memory the smallest of the 2 values. Usefull for projections or symetrisation macros.
MINIMAX: MINIMAX n1 n2 Load the value of the minimum and the maximum points that will be used for peak-picking. These value are loaded by the MAX command.
MINITER: Secondary iteration number for two steps minimisation in GIFA. Number of iterations used for the line-minimization during one step of the MaxEnt iteration. In a MaxEnt run, the number of FT's per iteration is MINITER + 2 Also used by other iterative process LINEFIT AUTOPHASE
MINUS: Sets to zero the positive parts of the signal
mkdbppm: Macro to generate a ppm DBM file from a ppm ascii file mkdbppm dbm_ppm_filename ascii_ppm_filename the ascii ppm file has the following free-format: PPM residu_name residu_number atom_name ppm_value linewidth_value
MODIFYSIZE: MODIFYSIZE si1 si2 {si3} Used mostly for hacking Permits to modify the leading sizes of a 2D or a 3D data-set, provided the product of the sizes : si1*si2{*si3} is equal to the product of the old ones. Does not actually modify the data.
MODIF_AMOEBA: MODIF_AMOEBA crdf1 crdf2 nopeak Assign the pixel at coordinates crdf1 crdf2 to the amoeba of the peak nopeak. The pixel coordinates crdf1 and crdf2 are given in index. Setting a nopeak of zero removes that pixel from the amoeba definition.
module: obsolte, use MODULUS instead
MODULUS: MODULUS is used to calculates the modulus of the spectrum. In 2D, will only works for fully Hypercomplex data-sets (itype == 3) or for data-sets complex in F2 (itype == 1) not for data-set complex in F2 (itype == 2). In this last case, you should use FLOP before doing MODULUS.
MONOPOINT: Permits to click once on the data-set. The top value on the point stak : context variables, $POINTX[1], $POINTY[1] and $BUTTON are set accordingly. If $NPOINT is zero (after a POINT_CLEAR) it is set to 1, unchanged otherwise. Useful for macros.
more: as in unix
MORPHOB: internal value for BCORR 3 algorithm
MORPHOS: internal value for BCORR 3 algorithm
MSKINTEG: integrates the current 2D data buffer using the last defined amoeba mask. The results are put into the peak list.
mskread: mskread file_name read the peak table and the amoeba written with mskwrite for integration with mskinteg appends extensions .pek and .amb to file_name
mskwrite: mskwrite file_name write the peak table and the amoeba for latter integration with mskread and mskinteg appends extensions .pek and .amb to file_name
MULT: MULT x Multiply data-set by a scalar.
MULTDATA: Multiplies point by point, the content of the current working buffer with the content of the DATA buffer. Permits to realize convolution product. Works in 1D, 2D, in real, complex and hypercomplex modes.
MULTIPOINT: Permits to click several time on the data-set. Similar to POINT, but no output is generated. The values of the pseudo-variables $NPOINT, $POINTX[1], $POINTY[1] and $BUTTON are set accordingly. Useful for macros.
MUNSET: munset list_of_variable_name * Removes all the variables which names are found in list_of_variable_name from the variable table. The list is terminated by a * sign. Note that no $ sign are needed.

Back to Alphabetical List

MACRO

MAX

MAXDATA

MAXENT

MAXENTCONT

MEDIAN

MEMORY

MESSAGE

METH

MINDATA

MINIMAX

MINITER

MINUS

mkdbppm

MODIFYSIZE

MODIF_AMOEBA

module

MODULUS

MONOPOINT

more

MORPHOB

MORPHOS

MSKINTEG

mskread

mskwrite

MULT

MULTDATA

MULTIPOINT

MUNSET