Software Directory

A computing resource (a web server and a database), Repeats in Protein Sequences (RPS), has been created. Using RPS, users can obtain useful information regarding identical, similar and distant repeats in protein sequences, check the frequency of occurrence of the repeats in several sequence databases, and view the three-dimensional structure of the repeats using the Java visualization plug-in Jmol.

Printing utility for Rietveld data and powder diffraction

Plot of data from Rietveld method programs. Read FAT-Rietan files as well as DBWS, GSAS output Postscript.

Calculates spatial variation of R-factor statistics.

A tool for analyzing small-angle neutron scattering (SANS) data using analytical model functions. Available also from author on request. The distribution includes the source code, the model library and the user manual.

Sadian Searches for Atomic DIstances and ANgles in crystal structures. [W.H. Baur & D. Kassner: Sadian90 prepares input for DLS-76 (and does other things as well). Z. Krist. Suppl. Issue, (1991), 3, 15].

The program allows loading of individual protein monomers or oligomeric structures which can be displayed and oriented as rigid bodies in a molecular graphics viewer. A shape object restored from small-angle scattering data can also be displayed, enabling the user to arrange the protein molecules to fit. For the loaded model, the small-angle scattering can be evaluated and compared to experimental scattering data.
Rigid body refinement of the loaded model has been implemented by means of a Monte-Carlo approach which uses the fit between model-derived and experimental scattering data as target function.

Scientific Applications on Linux references. SAL is copyrighted by Dr. Herng-Jeng Jou and Kachina Technologies, Inc. and it can be freely redistributed under GPL version 2 or later, or otherwise as stated by the owners of the individual files included in SAL.

Sequence Alignment and Modeling System

Benchmark for Crystallography by the San Diego Supercomputing Center

Multan-based program package: i Random-starting multisolution direct methods; ii Automatic Patterson analysis for heavy-atom containing structures; iii Combination of Patterson and direct methods; iv Automatic detection and solution of superstructures; v Resoving enantiomorphous phase ambiguity; vi Solving heavy-atom substructures for proteins.

Refinement of various parameters of III-V and II-VI semiconductors (ZnS) and elemental (diamond) semiconductors. To refine parameters in the harmonic, anharmonic and charge transfer approximations. Refines individual thermal, scale, extinction parameters and the charge transfer from one atom to the other in ZnS type structures. Calculates the real and imaginary phase parts FA and FB of the structure factors. Includes Bijvoet differences in the analysis. Averages the Bijvoet equivalent reflections, etc., etc.

Program for the refinement of various parameters of III-V and II-VI semiconductors (ZnS and elemental (diamond) semiconductors. To refine parameters in the harmonic, anharmonic and charge transfer approximations. Refines individual thermal, scale, extinction parameters and the charge transfer from one atom to the other in ZnS type structures. Calculates the real and imaginary phase parts FA and FB of the structure factors. Includes Bijvoet differences in the analysis. Averages the Bijvoet equivalent reflections, etc., etc.

Program computes Hauptman's three-phase structure invariant estimate for SAS data [omega = ph(h)+ph(k)+ph(l)]. Program Prequires 6 distinct magnitudes [E(h),E(k),E(l),E(-h),E(-k), E(-l), where h+k+l=0] and chemical composition of the cell

All That SAS - a data analysis program suite freely available to the research community by Dmitri I. Svergun, Michel H.J. Koch, Vladimir V. Volkov, Michael B. Kozin, Marc Malfois, Peter V. Konarev, Maxim V. Petoukhov, Anna V. Sokolova

A new software tool,available within the SASSIE software suite, designed to assist in planning small-angle neutron scattering experiments with contrast variation on protein and nucleic acid complexes.

A novel software platform for the analysis of biological small-angle scattering.

An interactive analytical program for small-angle X-ray scattering measurements of solutions