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cadzow

cadzow n_of_line n_of_iter apply the cadzow procedure to remove noise from the current FID. should be followed with an FT or an LP-SVD analysis
see also : ORDER SVDCLEAN1


calib

interactive permits to assign chemical shift to a given point will change the offset
see also : FREQ OFFSET point SPECW UNIT


CALIBDI

CALIBDI distance_ref rate_ref Sets the reference distance to a reference relaxation rate. Used when computing interspin distances from nOe build-up measurements.
see also : METH RELAXRATE


CCOLOR

ccolor n If n = 1 color plots (command CDISP2D) are displayed in color, if n = 0 color plots are displayed in B&W mode
see also : CDISP2D COLOR SCOLOR


CD

CD new_directory_path Changes the current working directory.
see also : ls more pwd rm SH vi vim vip


cdisp

obsolete, for compatibility

CDISP2D

CDISP2D 0/1 When CDISP2D is 1 the window displaying the contour plot of the 2D buffer is activated on the graphic screen in 2D.
see also : BCOLOR CCOLOR CLEAR COLOR DISP1D DISP2D DISP3D dispcont LEVEL LOGA SCALE SHOWC STPL STPL? super2d


center

center $f1 { $f2 { $f3 } } centers the zoom window on the coordinates the zoom window is kept with the same size

CHECK3D

This command enters a interactive mode in which the user can choose the different parameters used for a 3D display. Only the cube is shown for speed convinience. DISP3D must have been previously set to 1.
see also : DISP3D REF3D


CHEMS

Obsolete command, has been superseded by mkdbppm This command is an help for constructing chemical shift files to be used with the SIMUNOE command.
see also : SimSpect2D SIMUNOE


choose_scolor

to choose interactively the show color

CHSIZE

CHSIZE SI1 { SI2 { SI3 } } Change size of data, zero-fill or truncate. DO NOT change the value of OFFSET and SPECW, so EXTRACT should always be preferred on spectra (unless you know exactly what your are doing).
see also : EXTRACT lshift MODIFYSIZE rshift size


CLEAR

CLEAR 0/1 When set to 0, the 1D spectrum displayed by the current command, is put on the top of the currently displayed spectrum. Permits to add many spectrum images on the same display. When set to 1, the displat reacts in the standard fashion.
see also : COLOR REF UNREF


CLOSE

CLOSE file_name Closes the file that was previously OPENed.
see also : CONNECT FPRINT OPEN


CLOSEBUTTON

This command closes the current menu bar, and all the associated opened menu box. It is equivalent to closing it with the graphical close box.
see also : BUTTONBOX CLOSEFORM


CLOSEFORM

CLOSEFORM #id This command closes the FormBox, which id is #id The context $WIDGET when evaluated wihtin a form, contains the #id of the current form.
see also : CLOSEBUTTON FORMBOX


COL

Extracts a 1D column (along F1 axis) from the active 2D data-set, and displays it in the 1D window. The row will be available as a 1D data set when going from 2D to 1D
see also : colint DIAG DIM PLANE ROW rowint VERT


colint

interactive permits to choose columns interactively on a 2D by clicking on the data-set
see also : COL ph2dc planeint ROW rowint vertint


COLOR

COLOR index window Defines the current color used for display. The chosen color remains until the next COLOR command. index is : 1:white 2:red 3:yellow 4:green 5:cian 6:blue 7:purple 8:black Window is : 1:1D 2:disp 3:contour 4:3D
see also : BCOLOR CCOLOR CDISP2D DISP1D DISP2D DISP3D SCOLOR


CONCAT

CONCAT file_name Appends the content of file_name to the current data-set in memory. Work with 'H' files
see also : ADDH READH


CONFIG

Output to the terminal the actual configuration of the system dependent parameters : -Licence being used -Version number -Sizes of the different static buffers -Operating System (VMS or UNIX) -Graphic manager (X_Windows or VWS) -Plotter driver (HP-GL or Postscript)
see also : list MEMORY PLOTTER size VARIABLES


conjg

set up for Conjugated Gradient algorithm for MAXENT
see also : ALGO gad gifa


CONNECT

CONNECT file_name The journaling of all the actions, performed by GIFA is directed to the file_name. Journaling is resumed to the standard gifa.log files with DISCONNECT.
see also : CLOSE DISCONNECT LOG OPEN


cont

obsolete, for compatibility

CONTEXTS

List of the internal GIFA variables (contexts): $_ value of the next parameter present on the calling line. CANNOT BE USED WITHIN EVALUATED EXPRESSIONS. if the following command is used : @test 3 test.001 within the file test, $_ will be 3 the first time and test.001 the second time. If no value is present on the calling line, the user will be prompted for the value $ABSMAX current value of ABSMAX $ARG True (1) if arguments are present on the calling line (within macro only) $BUTTON 1,2 or 3 depending on which mouse button was last clicked $CALIBDI[1] the current calibrating distance, as defined with the CALIBDI command $CALIBDI[2] the current calibrating relaxation rate, as defined with the CALIBDI command $CCOLOR current value for CCOLOR $CDISP2D current value of command CDISP2D $CHI2 value of the chi2 returned by the last command : MAXENT, LINEFIT, RT->PK $COL index of the last extracted column in 2D $COLOR current value for COLOR $CONFIG_GRAPH is true if graphic is possible (X_window is connected) $CONFIG_OS The system type, as returned by the CONFIG command $CONFIG_PLOT The plot driver, as returned by the CONFIG command $CONFIG_WIN The window manager, as returned by the CONFIG command $CX current value for CX $CY current value for CY $CZ current value for CZ $C_ABSMAX value of ABSMAX of the currently JOINed dataset $C_DIM value of DIM of the currently JOINed dataset $C_FREQ value of FREQ of the currently JOINed dataset $C_FREQ1 value of FREQ_1D of the currently JOINed dataset $C_FREQ2 value of FREQ_2D of the currently JOINed dataset $C_FREQ3 value of FREQ_3D of the currently JOINed dataset $C_HEADER last value accessed with the GETHEADER command $C_JOINED is if there is a currently JOINed dataset, 0 otherwise $C_OFFSF1 value of OFFSET_1 of the currently JOINed dataset $C_OFFSF2 value of OFFSET_2 of the currently JOINed dataset $C_OFFSF3 value of OFFSET_3 of the currently JOINed dataset $C_SIZEF1 value of SI1 of the currently JOINed dataset $C_SIZEF2 value of SI2 of the currently JOINed dataset $C_SIZEF3 value of SI3 of the currently JOINed dataset $C_SPECWF1 value of SPECW_1 of the currently JOINed dataset $C_SPECWF2 value of SPECW_2 of the currently JOINed dataset $C_SPECWF3 value of SPECW_3 of the currently JOINed dataset $C_TYPE value of ITYPE of the currently JOINed dataset $DIM current value of DIM $DISP1D current value of command DISP1D $DISP2D current value of command DISP2D $DISP3D current value of command DISP3D $DIST the result of the last DIST command $FND_PK gives the index of the found entry (FIND) $FND_PK_DST gives the distance to target of the found entry (FIND) $FREQ main frequency (1H) of the spectrometer $FREQ_1D frequency in 1D (in MHz) $FREQ_1_2D frequency in 2D in F1 (in MHz) $FREQ_1_3D frequency in 3D in F1 (in MHz) $FREQ_2_2D frequency in 2D in F2 (in MHz) $FREQ_2_3D frequency in 3D in F2 (in MHz) $FREQ_3_3D frequency in 3D in F3 (in MHz) $GB1 value of gb in F1 (in Hz) $GB2 value of gb in F2 (in Hz) $GB3 value of gb in F3 (in Hz) $GIFAPATH current PATH used for macro, set by th SETPATH command $HOME equivalent to the $HOME variable in UNIX $ITYPE_1D value of itype in 1D $ITYPE_2D value of itype in 2D $ITYPE_3D value of itype in 1D $LB1 value of lb in F1 (in Hz) $LB2 value of lb in F2 (in Hz) $LB3 value of lb in F3 (in Hz) $LEVEL current value of command LEVEL $LICENCE The licence as returned by the CONFIG command $LOGA current value of command LOGA $MAX[1] value of last computed max computed with the command MAX $MAX[2] value of last computed min computed with the command MAX $MEM_MAX The larger data set available, as returned by the CONFIG command $MEM_PRO_1D The size of the protected 1D area, as returned by the CONFIG command $MEM_PRO_2D The size of the protected 2D area, as returned by the CONFIG command $MEM_PRO_3D The size of the protected 3D area, as returned by the CONFIG command $NAME name of the current data-set $NAR number of A.R. coefficients as listed by ARLIST $NOISE value of the noise, as given by the NOISE command $NPK1D The number of entries in the 1D peak table $NPK2D The number of entries in the 2D peak table $NPK3D The number of entries in the 3D peak table $NPOINT The number of entries in the point stack $NRT Number of root as listed by RTLIST $NSVD Number of root as listed by SVDLIST $OFFSET_1D spectral offset in 1D (in Hz) $OFFSET_1_2D spectral offset in 2D in F1 (in Hz) $OFFSET_1_3D spectral offset in 3D in F1 (in Hz) $OFFSET_2_2D spectral offset in 2D in F2 (in Hz) $OFFSET_2_3D spectral offset in 3D in F2 (in Hz) $OFFSET_3_3D spectral offset in 3D in F3 (in Hz) $ORDER current value for ORDER $PH0 0th order of the last phase correction $PH1 1st order of the last phase correction $PK1D_A[i] amplitude of the ith entry in the 1D peak table $PK1D_F[i] position (in index) of the ith entry in the 1D peak table $PK1D_P[i] phase of the ith entry in the 1D peak table $PK1D_W[i] width (in index) of the ith entry in the 1D peak table $PK2D_A[i] amplitude of the ith entry in the 2D peak table $PK2D_ERR[i] amplitude error as reported by INTEG. $PK2D_F1F[i] F1 position (in index) of the ith entry in the 2D peak table $PK2D_F1W[i] F1 width (in index) of the ith entry in the 2D peak table $PK2D_F2F[i] F2 position (in index) of the ith entry in the 2D peak table $PK2D_F2W[i] F2 width (in index) of the ith entry in the 2D peak table $PK3D_A[i] amplitude of the ith entry in the 3D peak table $PK3D_F1F[i] F1 position (in index) of the ith entry in the 3D peak table $PK3D_F1W[i] F1 width (in index) of the ith entry in the 3D peak table $PK3D_F2F[i] F2 position (in index) of the ith entry in the 3D peak table $PK3D_F2W[i] F2 width (in index) of the ith entry in the 3D peak table $PK3D_F3F[i] F3 position (in index) of the ith entry in the 3D peak table $PK3D_F3W[i] F3 width (in index) of the ith entry in the 3D peak table $PKNAME The name used by the last PKREAD / PKWRITE command $PLANE[1] axis of the last extracted plane in 3D $PLANE[2] index of the last extracted plane in 3D $PLOTAXIS[1] current value for the unit used in PLOTAXIS $PLOTAXIS[2] current value for the tick distance in x axis $PLOTAXIS[3] current value for the tick distance in y axis $PLOTOFFSET[1] current value for plot offset on X axis $PLOTOFFSET[2] current value for plot offset on Y axis $POINTX[i] X coordinates (in index) of ith point in the point stack $POINTY[i] Y coordinates (0..1 in 1D; in index if 2D) of ith point in the point stack $RANDOM a random variable in the range 0..1 with equiprobable distribution $RANDOMG a random variable with normal law, unit variance and zero mean $RANDOMZ same as $RANDOM but resets the random series $RELAX the result of the last RELAXRATE or SLOPE commands $RCRYST the result of the last RCRYST command CALIBDI $ROW index of the last extracted row in 2D $SCALE current value of the context SCALE $SCOLOR current value of the context SCOLOR $SHIFT value of the offset, as given by the SHIFT command $SI1_1D size of the 1D buffer. $SI1_2D size in F1 of the 2D buffer $SI1_3D size in F1 of the 3D buffer $SI2_2D size in F2 of the 2D buffer $SI2_3D size in F2 of the 3D buffer $SI3_3D size in F3 of the 3D buffer $SIGN current value of command SIGN $SPECW_1D spectral width in 1D (in Hz) $SPECW_1_2D spectral width in 2D in F1 (in Hz) $SPECW_1_3D spectral width in 3D in F1 (in Hz) $SPECW_2_2D spectral width in 2D in F2 (in Hz) $SPECW_2_3D spectral width in 3D in F2 (in Hz) $SPECW_3_3D spectral width in 3D in F3 (in Hz) $SUMREC value returned by the last SUMREC command $UNIT current value for UNIT $VAR_MAX The total number of user variable available, as returned by the CONFIG command $VERSION The current version, as returned by the CONFIG command $VHEIGHT current value of command VHEIGHT $WIDGET The id of the current graphic form $ZONE[1] lower F1 coord. of the mouse-selected region (in index) $ZONE[2] lower F2 coord. of the mouse-selected region (in index) $ZONE[3] upper F1 coord. of the mouse-selected region (in index) $ZONE[4] upper F2 coord. of the mouse-selected region (in index) $ZOOM 1 if in ZOOM mode $ZOOM_1D[1] left coordinate of the 1D zoom window (in index) $ZOOM_1D[2] right coordinate of the 1D zoom window (in index) $ZOOM_2D[1] lower F1 coordinate of the 2D zoom window (in index) $ZOOM_2D[2] left F2 coordinate of the 2D zoom window (in index) $ZOOM_2D[3] upper F1 coordinate of the 2D zoom window (in index) $ZOOM_2D[4] right F2 coordinate of the 2D zoom window (in index) $ZOOM_3D[1] "left" F1 coordinate of the 3D zoom window (in index) $ZOOM_3D[2] "right" F1 coordinate of the 3D zoom window (in index) $ZOOM_3D[3] "left" F2 coordinate of the 3D zoom window (in index) $ZOOM_3D[4] "right" F2 coordinate of the 3D zoom window (in index) $ZOOM_3D[5] "left" F3 coordinate of the 3D zoom window (in index) $ZOOM_3D[6] "right" F3 coordinate of the 3D zoom window (in index)
see also : FUNCTIONS MACRO VARIABLES


CONTROLS

Control structures are available in the macros file : GOTO - one line IF - multiple line IF - FOR loop - FOREACH loop - WHILE loop macros can be called from within macros, up to 9 levels of nesting. No recursivity is allowed.
see also : CONTEXTS ERROR FOR FOREACH FUNCTIONS GOTO IF MACRO SETPATH SETPROMPT VARIABLES WHILE


correct1st

no parameter corrects for the 1st point by dividing it by 2
see also : FT


correctppm

to correct the ppm/Hz computation in Gifa with version < 4.10 in Gifa version < 4.10 , (i.e up to 4.09) computation of ppm and Hz is slightly wrong, by a factor (size-1)/size. This macro corrects the internal values of specw and offset to give a correct computation of ppm and Hz. however, ppm definition will shift a little for spectral region at high field. so you might want to recalibrate afterward. It should be applied only ONCE to a data-set. Since it modifies the spectral parameters of the data-set, this data-set, if wrote onto a file will be wrong when read with a corrected version of Gifa. so the following procedure is proposed : Do not touch to your files, version 4.10 should be available by sept. 1996 Rather read your files, and apply correctppm after reading, so that the in-memory file is correct. Do not write it back, at least not on file you wish to use later on. Note also that peak-files are stored in ppm format so peak-tables stored in corrected ppm, will be Ok when read with the corrected version of Gifa. If you have already peak-tables that you wish to keep, and you want to correct the ppm values, do the following : read file ; get file pkread peaks.old ; load peaks correctppm ; peaks won't move because they are internally in index ! pkwrite peaks.new ; store corrected peak values. next time you use it read file correctppm pkread peaks.new ; is fine

CX

CX x Size in centimeters in the x-axis used for the graphic windows and for the plot. Used by PLOT and STPL
see also : CY CZ PLOT STPL STPL?


CY

CY y Size in centimeters of the y-axis used for the graphic windows and for the plot. Used by PLOT and STPL.
see also : CX CZ PLOT STPL STPL?


CZ

CZ z Size in centimeters of the z-axis used for 3D display.
see also : CX CY DISP3D PLOT3D