The Gifa v4.2 program is a software meant for processing and
analysis high resolution NMR spectra, in 1D, 2D and 3D.
It includes :
Classical processing includes :
o Full capabilities in 1D, 2D and 3D processing.
o Full array of apodisation functions (shifted sine-bells and
squared sine-bells; exponential; Gaussian; trapezoid, and
o Fast Fourier transform (direct and inverse; real, complex,
and hypercomplex). Hilbert transforms.
o Zero-filling and truncation.
o Phasing of 1D, 2D and 3D spectra.
o Processing in memory (for regular data size) or on disk (for
very large data-set) with similar syntaxes
o Non-limited size data-set with optimised file access
o Very fast processing : (figures not garantied)
* 15.5" on SGI INDY PC (100MHz)
* 12.6" on IBM Risc 6000-560
* 12.3" on SUN Sparc 20
* 10.5" on SGI INDY (174MHz)
* 10" on HP 715/80
* 9.5" on PC Pentium 133MHz Linux
* 7.5" on HP 735/99
* 6.5" on SGI-O2 R5000-PC
* 5.06" on Pentium Pro 200 Linux
for the complete processing of a 512x2048 data points data-
set, including :
-exponential windowing in F2, shifted sine bell in F1.
-hypercomplex FT with zero-filling in F1 and phasing in both axes.
-cubic spline baseline correction through 5 points in F2.
o Post-processing filters; module, real part extraction,
absolute value, smoothing, etc...
o Complete baseline correction module (linear, cubic spline
correction, and a comprehensive polynomial module with
automatic peak detection).
o Extraction of sub-spectra for local processing.
o Simulation of pseudo data-sets. Simulation of 2D NOESY from
intensity files (CORMA type)
o Addition, multiplication of data-sets.
o 2D Displays in -density mode -contour mode -stacked plot mode
o 3D Display in 3D perspective
o Random access to rows, columns, diagonals or projections in
o Random access to planes and rows in any direction or diagonal
in 3D mode.
o Multi-windowing facilities : up to 4 active windows in the
same time, many passive windows.
o Fast zoom mode - Fast interactive phasing mode.
o Complete plotting facilities. On screen : 1D plots; 2D : full
colours density maps, zoom, contour plots and stacked plots; 3D
: automatic series of 2D plots, 3D graphics. All 1D, 2D and 3D
graphics may be sent to a plotter (HP-plotter or PostScript
laser printer). Several plots may be disposed on the same sheet
of paper, and plot files can be stored separately.
Special processing includes :
o A protein assignment module is available for 2D homonuclear spectra.
Completely written in the macro language.
o Maximum Entropy processing of 1D as well as 2D data-sets. A
generalised iteration scheme, (Gifa stands for Generalised
Iterative Fixed-point Algorithm) as well as more classical
algorithms : Gull & Daniel, conjugated gradients.
o Maximum Entropy deconvolution of Lorentzian line-shape, of J-
coupling pattern, or of any user-provided function.
o Comprehensive Linear Prediction module, including Burg, LP-
SVD, forward and backward methods, etcÉ
o Processing of DOSY experiments,using the Maximum Entropy technique.
o Integrated processing of NOESY build-up curves, permitting to
accurately evaluate distances.
o Automatic peak-picker in 1D 2D and 3D; Automatic peak
integrator in 1D and 2D.
o Line fitting of mixed Lorentzian and Gaussian Line Shapes
o Several file formats are available, notably a FT-NMR(tm)
compatible format, a MATLAB(tm) compatible format, a compressed
format, a generic file format, permitting direct random access,
and several others.
A Complete set of Macro :
o A complete graphic user interface written in the macro
o Calibration, integration, peak-picking, etc..
o Fast interaction with the mouse on 2D and 3D
o Help for attribution, on screen and on plotter
o Easily extensible with the control language
The User Interface is characterised by :
o Most command are available through a graphic interface
o Interactive commands for beginners as well as fast entry mode
for advanced users
o Complete on-line HELP.
o Comprehensive manual.
o Versatile command parser which permits to build macro
commands with alias, tests, local and global variables, loops,
graphic interaction and display capabilities, support for data-
bases and associative arrays.
o graphical interface completely modifiable and definable by
o Possibility to run in interactive mode as well as Batch mode
o The operating system is fully available from Gifa.