Back to Alphabetical List



ABS

Computes absolute value of data-sets, Works only on real data-sets (itype=0) related contexts : $ITYPE_1D $ITYPE_2D $ITYPE_3D
see also : MODULUS REAL


ABSMAX

Absolute factor to which scale refers to for displaying and plotting. Usually ABSMAX holds the largest point of the data-set, but you can set it by hand in order to do absolute plots. ABSMAX is recomputed whenever the data is changed. You can force the ABSMAX to be recomputed by setting it to zero. You can also hampers the recomputation of absmax (which can be VERY long (on 3D for instance)) by setting it to a standard value at the end of the command line related contexts : $ABSMAX
see also : DISP1D DISP2D DISP3D MAX SCALE


ADD

ADD name_of_file -or- ADDC name_of_file permits to add to the current data-set the content of the file name_of_file, which is in standard format. Works for both 1D, 2D and 3D data-sets. related contexts : $NAME
see also : ADDDATA ADDH MULT READ


ADDBASE

ADDBASE constant Removes a constant to the data. The default value is the value of SHIFT (computed by EVALN). related contexts : $SHIFT
see also : EVALN SHIFT


ADDC

Equivalent to ADD
see also : ADD


ADDDATA

Add the contents of the DATA buffer to the current data-set. Equivalent to ADD but in-memory.
see also : ADD ADDH MAXDATA MINDATA MULT MULTDATA PUT


ADDH

ADDH name_of_file Same as ADD, with H format files.
see also : ADD ADDDATA CONCAT MULT


ADDNOISE

addnoise noise seed add to the current data-set (1D, 2D, 3D) a white-gaussian, characterized by its level noise, and the random generator seed. related contexts : $NOISE $RANDOM $RANDOMG $RANDOMZ
see also : EVALN SIMU SIMUN


ALERT

alert text Creates a graphic alert box displaying the text. User must click in the alert box to continue. Works only if the graphic mode has been intialzed by isuing, at least once, a graphic command.
see also : ERROR PRINT


ALGO

Context used to describe the current algorithm Algo is a number of the form abc where a, b and, c are the decimal digits. c: 0 Gull and Daniel equation for Entropy 1 GIFA equation for Entropy 2 steepest descent equation is used 3 conjugate gradient is used b: 0 single step iteration 1 line-maximization using parabolic fit. 2 : line-maximization using bracketing before parabolic fit. a: 0 no Wu correction 1 Wu correction is applied. related contexts : $ALGO
see also : conjg gad gifa MAXENT


ALPHA

alpha a This context is the angle along the OZ axis by which the cube is rotated during a 3D display with the DISP3D/REF3D set of commands
see also : BETA DISP3D GAMA


APPLY

APPLY what_to_apply Apply a windowing function to the data-set. You can apply : FILTER : applies the filter used during MaxEnt iterations, depends on LB, GB, JCONS, FILTER WINDOW : applies the window used during MaxEnt iterations.
see also : FILTER GB GET JCONS LB PUT SHOW WINDOW


APPROX

Used in the BCORR 3 module, to choose the way the baseline is estimated. 0 : with ITERMA2 times a moving average filtering on a window of size WINMA2. 1 : with a Legendre polynomial approximation of degree DEGRE. +10 : with a linear interpolation of signal before approximation. +100 : with an 'elastic effect' that is a rude way to prevent from burying the weak lines.
see also : BCORR BCORRP?


apropos

apropos topic for GIFA on_line help Search the string "topic" in all the help files available
see also : help


apsl

automatic 1D phase correction APSL method A.Heuer J.Magn.Reson. 91 p241 (1991) uses the data buffer you may want to adapt : s_wdth : ration of line width to spectral width used for computing phases p_wdth : ration of line width to spectral width used for broadening for peak picking npk : minimum number of peaks needed for phasing nfrst : the number of peaks used for first approx
see also : apsl_cp PH PHASE


apsl_cp

apsl_cp i sz computes the phase of the peak centered on i, using +/-sz points the phase of the peak is returned as a global variable called $returned between -180 and 180 i has to be odd ! used as a routine by the macro apsl
see also : apsl


AR->DT

AR->DT size n Extend the data-set up to size points long by predicting the missing data points, using linear prediction. n = 1 : following points predicted -> forward prediction n = 2 : previous points predicted -> backward prediction related contexts : $NAR $SI1_1D
see also : BURG DT->AR ORDER SVD->AR


AR->RT

AR->RT n Solve the prediction-error polynomial, calculated from the autoregressive coefficients. This is the third step of the LP-SVD method. n = 1 : forward coefficients are used to extracted forward roots n = 2 : backward coefficients are used to extracted backward roots n = 3 : both set of roots are computed related contexts : $NRT $SI1_1D
see also : AR->RT2 ARLIST ORDER RT->AR SVD->AR


AR->RT2

AR->RT2 n Equivalent to AR->RT, but seems to be more stable for very large polynomial. related contexts : $NRT $SI1_1D
see also : ARLIST ORDER RT->AR SVD->AR


AR->SP

Calculate the modulus of spectrum from the autoregressive Burg coefficients. This is the so-called Burg spectrum, (sometimes unfortunately called mem spectrum). The spectrum is computed to the size of the current 1D buffer size.
see also : DT->AR ORDER


ARLIST

ARLIST n i j list the autoregressive coefficients from entry i to entry j. n = 1 : forward coefficients n = 2 : backward coefficients related contexts : $NAR
see also : AR->DT AR->RT RT->AR


ASSIGN

The assignment module implements a set of very simple assignment tools. It is completely written in the Gifa macro language, and as such can be fully adapted to your needs. Right now, it is principally aimed toward protein and peptide assignment. You enter the module by choosing 'Assignment' in Mode menu. Here is a simple 'recipe' on how to use this module: 1) get a set of nice processed homonuclear 2D experiments somewhere on the computer system. 2) create a new project, enter the primary sequence, and link all your nice 2D into the spectra directory; then read-in the TOCSY. 3) peak-pick the TOCSY spectrum, at least on the finger print region and copy it over into the assignment data-base, eventually redo so for NH-side chain regions. 4) use the marker tool to note peak alignments, eventually confirm by "showing" also the NOESY, or a TOCSY from other experimental conditions. 5) once a spin system is found, and noted with one or several markers, eventually create the corresponding additional peaks with marker tool, create spins, and put them in the special "build-list"; 6) promote the spin-list to a spin-system 7) go back to 4) as long as there are spin-systems to assign. 8) load the NOESY in place of the TOCSY 9) use the NH-NH region and the NH-Ha region to do the sequential assignment, use the marker tool again to create new NOESY peaks in the data-base. Check peaks and spins with the find peak and find spin tools, use edit peak to add peaks in the NOESY data base. 10) once a sequential is found, modify the spin systems accordingly 11) go back to 9 as long as the sequential is not finished 12) assign all remaining NOESY peaks. 13) output the NOESY peaks in the form of a XPLOR constraint list (this will become automatic soon !) Thirteen steps, not such a big deal after all !

AXIS

AXIS axis_to_draw with axis_to_draw : [ NONE | F1 | F2 | F12 ] Determines how coordinates will be drawn on screen Axes are drawn on the 1D, the 2D density and the 2D contour windows. The unit is determined by the command UNIT related contexts : $AXIS $UNIT
see also : CDISP2D DISP1D DISP2D PLOTAXIS PLOTAXIS? UNIT


AXIS3D

axis3d fx where x is 1, 2, 3, 12, 13, or 123 This context holds the focal length that will be used for computing a 3D display with the DISP3D/REF3D set of commands
see also : CHECK3D DISP3D REF3D