PRESENTATION
The Gifa program is a multi-purpose NMR program. It is designed
for the processing, the display and the analysis of 1D, 2D & 3D NMR
data-sets.
The program includes all the classical processing, displaying and plotting
capabilities of an NMR program, as well as more advanced processing techniques
such as Maximum Entropy processing or Linear prediction. There is no actual
limit to the size of the data-set which can be processed. A complete macro
language permits to builds sophisticated processing. The Graphic User Interface
is fully designable and programmable by the user.
The program currently runs on several UNIX platforms. The graphics can be
displayed on X-Windows terminals. Plots are generated on postscript or HP-GL
devices.
This version V4.0 is now in final version, however it is evoluating all the
time, check our ftp server ! This version is distributed under a licence. There
is no fees for academic laboratories, however the licence requires that you
refer to Gifa in any published work which depend in some manner on the Gifa
program.
This program can be downloaded by anonymous FTP on Internet, the home site is
the following address : ftp://www.cbs.univ-montp1.fr/pub/gifa_v4
.
Previous released versions have been : 1.0 (Initial VMS Version), 1.1 (revised
version), 2.0 (first port to UNIX), 2.1 (first stabilised version), 2.5
(introduction of linear prediction, polynomial baseline correction), 3.0
(introduction of macro-language, on-file processing, etc...), 3.1 (new
peak-picker and line-fitter), 4.0 (Motif version, new user interface, new
language capabilities, new cache, extended line fitter). Several versions have
been used internally in our lab, and may have been released by mistake.
- Full capabilities in 1D, 2D and 3D processing.
- Full array of apodisation functions (shifted sine-bells and squared
sine-bells; exponential; Gaussian; trapezoid, and combinations).
- Fast Fourier transform (direct and inverse; real, complex, and
hypercomplex). Hilbert transforms.
- Zero-filling and truncation.
- Phasing of 1D, 2D and 3D spectra.
- Processing in memory (for regular data size) or on disk (for very large
data-set) with similar syntaxes
- Non-limited size data-set with optimised file access protocol.
- Very fast processing :
- 2'30" on Macintosh Centris 650 - running MachTen
- 36.3" on PC Am486DX4/100, 16 Mb memory - running Linux
- 17" on HP 725/50
- 15.5" on SGI-INDY PC
- 12.6" on IBM Risc 6000-560
- 12.3" on SUN Sparc 20
- 9.5" on PC Pentium 133MHz Linux
- 7.5" on HP 735/99
- 6.8" on SGI-INDY R5000-180MHz
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.
- Post-processing filters; modulus, real part extraction, absolute value,
smoothing, etc...
- Complete baseline correction module (linear, cubic spline correction, and
a comprehensive polynomial module with automatic peak detection).
- Extraction of sub-spectra for local processing.
- Simulation of pseudo data-sets. Simulation of 2D NOESY from intensity
files (CORMA type)
- Addition, multiplication of data-sets.
- 2D Displays in -density mode -contour mode -stacked plot mode
- 3D Display in 3D perspective
- Random access to rows, columns, diagonals or projections in 2D mode.
- Random access to planes and rows in any direction or diagonals in 3D mode.
- Multi-windowing facilities : up to 4 active windows in the same time, many
passive windows.
- Fast zoom mode - Fast interactive phasing mode.
- 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.
- A protein assignment module is available for 2D homonuclear
spectra.
Completely written in the macro language.
- 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.
- Maximum Entropy deconvolution of Lorentzian line-shape, of J-coupling
pattern, or of any user-provided function.
- Comprehensive Linear Prediction module, including Burg, LP-SVD, forward
and backward methods, etc...
- Integrated processing of NOESY build-up curves, permitting to accurately
evaluate distances.
- Automatic peak-picker in 1D 2D and 3D; Automatic peak integrator in 1D and
2D.
- Line fitting of mixed Lorentzian and Gaussian Line Shapes
- Several file formats are available, notably a FT-NMR® compatible
format, a MATLAB® compatible format, a compressed format, a generic file
format, permitting direct random access, and several others.
- A complete graphic user interface written in the macro language
- Calibration, integration, peak-picking, etc..
- Fast interaction with the mouse on 2D and 3D
- Help for attribution, on screen and on plotter
- Easily extensible with the control language
- Most command are available through a flexible graphic interface
- Interactive commands for beginners as well as fast entry mode for advanced
users
- Complete on-line HELP.
- Comprehensive manual.
- 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.
- Graphical interface completely modifiable and definable by the user.
- Possibility to run in interactive mode as well as Batch mode (display
less).
- The operating system is fully available from Gifa.