Spectroscopy

[*] GAMMA (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.
[*] Gifa V4 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.
[*] MEXICO 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 and plotting.
[*] OPIUM 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.
[*] New! PEST (Public EPR Software Tools) is a software for the acquisition and analysis of Electron Paramagnetic Resonance (EPR) data.
[*] Remote Microscope The Rem ote Microscope system allows users to access and control an optical microscope over the Internet using a Java applet
[*] SHELX-97 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 the 1960's.
[*] SIMPLTN (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.
[*] SIR92 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, )
[*] V : 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.
[*] What If (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.
[*] X-PLOR 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 control.
[*] xcosm 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.
[*] XEASY ($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.)
[*] XEMR 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. Some features:
  • 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 directions.
  • Cursors (with mouse) to mark points in spectrum and to calculate differences etc.
  • 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.
WARNING: the Software is in beta-test!
[*] XNMR 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.
[*] XtalView is a complete package for solving a macromolecular crystal structure by isomorphous replacement, including building the molecular model.