(a General Approach
to Magnetic resonance Mathematical Analysis) is a computer package designed
to facilitate construction of programs that simulate magnetic resonance
phenomena. GAMMA is NOT a computer program, it is a platform upon which one
can easily build programs. In many respects GAMMA is similar to a
subroutine library. Such libraries are commonly used in programming to
reduce the amount of labor needed in order to accomplish a simulation.|
is a computer
program designed for the processing and the visualization of 1D, 2D, and
3D NMR data-set. Gifa runs on differents UNIX computer systems (Hewlett
Packard, Silicon Graphics, IBM ...), with or without graphic display, in
interactive or batch mode. Gifa includes many poweful signal processing
methods such as Maximum Entropy, Linear Prediction, automatic Phasing,
line fiting, base line correction...etc. There are differents ways of
interacting with the software. The user may choose between a graphic, a
command line or a language interface.|
is a program for calculating lineshapes in the NMR spectrum of exchanging
species. Chemical exchange has usually been treated with the classic DNMR3
program. MEXICO extends this work, and is written in C for UNIX-based
computers. The program works by calculating a lineshape which can then
be imported into standard NMR processing software for display, comparison
is a console based program for the analysis of solution equilibria,
determination of chemical model, determination of equilibrium (stability,
formation, protonation, dissociation, association) constants using
potentiometry, UV/VIS spectrophotometry, NMR spectroscopy, polarography,
capillary zone electrophoresis and other useful methods. The data are
processed by means of the generalized nonlinear least squares method.|
Software Tools) is a software for the acquisition and analysis of Electron
Paramagnetic Resonance (EPR) data.|
The Rem ote Microscope system allows users to access and control an optical microscope over the Internet using a Java applet|
is a set of programs for crystal structure determination from single-crystal
diffraction data. The first version of SHELX was written at the end of
(SIMulation of PuLse and Two-dimensional NMR) is a spin-simulation program.
Simulations of NMR spectra can be performed for most NMR pulse sequences,
including both 1-D and 2-D (and higher D) NMR experiments. SIMPLTN can serve
as a tool for analyzing experimental data and designing new NMR experiments
as well as a learning/teaching tool. Any size of spin system possible, but
the practical limit may be 6 coupled spins. The output file can be converted
into a series of fids which can be imported directly into an NMR data
processing program (VNMR, FELIX, UXNMR) for processing and plotting, just
like experimental data.|
is a fully automated structure-determination program which is able to
solve the phase problem and to refine atomic parameters in a single
computer run by direct methods theory. To obtain a copy please contact
Dr Cascarano providing your ftp
address. (Dr. Gianluca Cascarano, Istituto di Ricerca per lo Sviluppo di
Metodologie Cristallografiche CNR, c/o Dipartimento Geomineralogico Campus
Universitario, 70124 Bari, Italy, Tel: +39-80-242624, FAX: +39-80-242591, )|
: Multidimensional Signal Processing for Magnetic Resonance. A general-purpose
software system for magnetic resonance imaging and spectral reconstruction,
processing, and analysis. It is intended not to be a comprehensive package
including every known algorithm, but rather as a basic package including
some of the popular reconstruction tools. Moreover, it is largely aimed
at providing a means for distribution of functions among researchers in
the MR community. V has been designed so that software development does
not require an immense knowledge of the internal operation of the program.
Rather, the programmer can develop individual functions indepently of V.
After validation and testing, these functions can be incorporated into
the V program with minimum modification.|
(Academic users are requested (but not obliged) to pay US$ 250,- or DM 400,-).
WHAT IF is written by G. Vriend as a tool for protein engineers, drug designers,
NMR, spectroscopists, and crystallographers. WHAT IF allows the molecular
engineer to sit in front of a computer terminal or better, a graphics workstation,
and ask questions that start with "What if ...." and then continue
for example with "...I mutated that valine into an isoleucine?".
The program can help the user by calculating the consequences of such a
mutation. To do so it can use a three dimensional relational protein database
in one, two, or three dimensions. It allows for quick evaluations of mutations
in terms of occupied space, Van der Waals contacts, hydrogen bridges, accessible
surfaces etc. The very fast access to the graphics system stimulates human
inspection of results. The program is set up in a very transparent way,
using many easy to use menu's. The user only needs to know the very few
basic options, plus the options he or she wants to use. So, although WHAT
IF offers more than two thousand options to the user, one only needs to
know very few of those in order to answer even elaborate questions.|
is a program system for computational structural biology (X-ray
crystallography and NMR). X-PLOR stands for exploration of conformational
space of macromolecules restrained to regions allowed by combinations of
empirical energy functions and experimental data. But it also stands for
exploration of modern concepts of structured programming in macromolecular
simulation. At the moment, xplor is being restructured, and it might go on
for a while. During this time, there will be no Linux binary releases etc.|
||X-ray NCSU Chemistry Facility
to use Linux for Crystallographic
Computing. Linux is used both for calculations and for Diffractometer
is an X-Windows interface to two Computational Optical Sectioning Microscopy (COSM) algorithms for removing out-of-focus light in 3-D
volumes collected plane by plane. The interface allows users to view and process multiple 3-D datasets within a simple mouse-driven environment.|
($200 for academic) is a UNIX/X-WINDOW program to display and
assign 2D, 3D, and 4D NMR spectra. Evaluation of 3D and 4D spectra is based
on the concept of "strips", i.e. parts of the spectrum the position of which
is defined in a corresponding 2D spectrum.)|
is a software package written for electron magnetic resonance (EMR)
spectroscopists. The program consists of the graphical front end which is
written using XForms -library, and the
libepr which contains all the spectrum manipulation and simulation routines.
WARNING: the Software is in beta-test!
- Load & Store spectra in libepr format. Conversion from Bruker (ESP),
Bruker (Aspect), X Y data and plain Y data.
- Graphical view of the spectra including overlay + zooming in X and Y
- Cursors (with mouse) to mark points in spectrum and to calculate
- Edit spectrum and measurement parameters.
- Zero & shrink parts of spectra.
- Addition (another spectrum and constant), multiplication by constant.
- Interactive shifting and scaling of (overlaid) spectra.
- Differentiate / integrate spectrum.
- Smoothing (9 point and symmetry).
- Forward & reverse Fourier transformations.
- Convolutions with other spectra or some smoothing functions.
- Baseline corrections (mark the background with mouse): polynomial and spline.
(also mean value subtract & calculation of noise level).
- Measurement (not yet fully implemented - will contain interface for Varian
and Bruker ER200 EPR/ENDOR/TRIPLE).
- Calculation of peak differences, position analysis, definite single and
double integration of peaks.
- Isotropic EPR simulation including asymmetric line width implementation
(m_i based anisotropy).
- Read / write / print isotropic simulation parameters
- Fitting of experimental and simulated spectra using Monte Carlo or
Simplex methods (variables are HFCs, line widths, line width asymmetry
parameters, etc.). Equivalence editor for fitting for issuing
dependencies between parameters.
- Exchange simulation using the Norris formula. The average life time of the
species may be included in the set of optimizable parameters.
- Exchange simulation using the Heinzer's method.
- Interface to XMGR graphics program for producing nice print outs of
spectra. Supports HPGL and postscript. This includes stack plots.
- Single crystal and powder simulation facilities. (Still only S = 1/2).
These can be added on top of any simulation method described above.
is a X11/Motif based program for processing and simulating exchange broadened
NMR spectra. Processing is only possible with data coming from Bruker NMR
spectrometers. Simulating, of course, is independent from the spectrometer
type. XNMR should run on any platform with at least X11R4 and Motif 1.1.
If possible, newer versions of X11 and Motif should be used. XNMR is Shareware.
See the README file for details.|
is a complete package for solving a macromolecular crystal structure by
isomorphous replacement, including building the molecular model.|