Crystallographic software list

SAAF 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.

Sacch3d

Sadian91 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].

SAFIR 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.

SaitoLab

SAL 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.

SAM Sequence Alignment and Modeling System

San Diego Benchmark Benchmark for Crystallography by the San Diego Supercomputing Center

SAPI 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.

SARA11 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.

SASdata analysis from biological macromolecules 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

SAS-OMEGA 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

SASSIE Contrast Calculator 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.

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

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

SaxsMDView The program performs a three-dimensional graphical representation for protein molecules along with the force vector (or vector potential) applying to each atom.

SAXSMorph Program to generate three-dimensional representative morphologies of two-phase systems using small-angle X-ray or neutron scattering data. The morphologies thus generated have the correct length scales and degree of connectivity with respect to the sample and are a useful visualization tool. The program also offers statistical analysis of the generated morphology and is user friendly and platform independent.

SCANPS protein sequence database scanning using

SCARECROW A graphics proram for the analysis and display of molecular dynamics trajectories.

SCAT331 For the generation and calculation of the X-ray structure factors and the real and imaginary parts of the structure factors of any crystalline system.

SCAT771 Having a set of h k l values and powder intensities, apply Lp and multiplicity corrections for any point group, and convert the intensity data into corresponding structure factors. Calculate the structure factors for the supplied set of h k l values, correct the structure factors for anomalous dispersion effects for 10 different wavelengths, calculate the real and imaginary parts of the structure factors, calculate the sin(theta)/lambda values and the atomic scattering factors of all the atoms that you specify in the structure and much more. EExists as GUI version named scat771win.

Scatfac X-ray atomic scattering factor display software which can display 1 to 2 elements on the screen. Can also output the data to an ASCII file.

SCATT771WIN If you have a set of h k l values and powder intensities, you would like to apply Lp and multiplicity corrections for any point group, and convert the intensity data into corresponding structure factors. You may want to calculate the structure factors for the supplied set of h k l values. You may want to correct the structure factors for anomalous dispersion effects for 10 different wavelengths. You may want to calculate the real and imaginary parts of the structure factors. You may want to calculate the sin(theta)/lambda values and the atomic scattering factors of all the atoms that you specify in your structure. You can do all these tasks with this program. Any number atoms (from 212 different kinds of atoms/ions) can be handled in your structures. The program can be wisely used for multiple tasks. There are options to suppress the application of multiplicity correction and absorption correction individually or in combination. Also, simulation of structure factors for a given set of h k l values can be done. No need to supply analytical coefficients, dispersion corrections – all data are pre-connected. Atom names and some preliminary info enough.

SCHAKAL SCHAKAL, written by Egbert Keller, is a program for the graphical representation of molecular and solid-state structure models.

SDP for Windows Complete crystallographic software package for small molecule structures, including data reduction, structure solution and refinement, calculation of derived parameters, real-time interactive graphics, presentation graphics and preparation of text and tables for publication. Windows 3.1, Windows 95 and Windows 98.

SDS Ordinary Structure Refinement Program

Searchmatch Search match program for use with the International Centre for Diffraction Data's Powder Diffraction File: - powerful search algorithm for multi-phase identification - lightning-fast search using raw data, peak data or a combination of the two - fully integrated Boolean PDF card retrieval and display - user database, with interface to Crystallographica - fully integrated peak search and background subtraction tools - powder pattern simulation, including multi-phase mixtures - reads most common file formats - if not just ask! - writes reports directly to Microsoft Word

SEQIO A package for reading and writing sequence files (JR Knight, UC Davis).

SETOR High-quality rendering of raster images of macromolecules that can undergo rotation and translation interactively .

SEXIE Calculation of Coordination Shells and Geometries

SF2CNS General purpose program to calculate CNS-formatted maps easily.

SFAC331 For the generation and calculation of the X-ray structure factors and the real and imaginary parts of the structure factors of any crystalline system. Highly useful for beginners in the field. Exists as GUI versions named sfac331win and sfac331_mix for mixed structures.

SFAC332 For the generation and calculation of the X-ray structure factors and the real and imaginary parts of the structure factors of any crystalline system. And many more jobs.

SFAC333 For the generation and calculation of the X-ray structure factors and the real and imaginary parts of the structure factors of any crystalline system. Many more jobs.

SFAC333, SFAC332 For the generation and calculation of the X-ray structure factors and the real and imaginary parts of the structure factors of any crystalline system. Plus other jobs.

SFAC334 For the generation and calculation of the X-ray structure factors and the real and imaginary parts of the structure factors of any crystalline system.Plus additional jobs.

SFAC334 For the generation and calculation of the X-ray structure factors and the real and imaginary parts of the structure factors of any crystalline system. Many more functions.

SgInfo A comprehensive collection of ANSI C routines for the handling of space group symmetry from Switzerland's ETH.

SHADE Estimates anisotropic displacement parameters for hydrogen atoms by combining a rigid-body analysis of the non-hydrogen-atom anisotropic displacement parameters (ADPs) with a contribution from internal atomic motion. Bibliography:

SHADE3 The SHADE web server has been updated to allow the use of ab initio calculations and experimental information. The resulting H-atom anisotropic displacement parameters are compared with neutron structures and other estimation approaches.

SHADOW Powder program. Peak fitting, see CCP14

ShakePSD To solve the structures of organic compounds automatically. Can discriminate whether a heavy-atom is included or not and can employ heavy-atom methods (Patterson function and search for all remaining atoms) or direct methods (tangent formula and/or minimal function).

SHAPE Drawing the external morphology (faces) of crystals and quasi-crystals. Also drawing of sections of crystals. The Professional edition (Windows only) includes two capabilities beyond those of the standard edition: quasi-crystals and sections/growth-zones.

Shape_CCMS Analysis of structure and chemistry at the molecular surface.

Shark frame grabber high quality digitisation of an image or diffraction pattern.

SHARP A Statistical Heavy Atom Refinement and Phasing program

SHELX-97 Set of programs for crystal structure determination from single-crystal diffraction data. Runs on all systems including DOS. See also SHELXS for PC versions.

SHELXL2013 Some of the improvements in SHELX2013 make SHELXL convenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data.

ShelXle ShelXle is a graphical user interface (GUI) for SHELXL. It combines an editor with syntax highlighting feature and a OpenGL visualization of the structure including electron density maps. The GUI is written in C++ using the Qt4 library and the Fourier transformation for the map is done using FFTW3 library.

SHELXS PC version (DOS and Windows) of the structure solution program SHELXS-86 by G. Sheldrick. Availability is restricted to registered users only. For registration as well as for versions for others systems. see SHELX-97.

Shift_plot Shift_plot may be useful for visual analysis of magnitudes of atomic shifts in refinement.

SIFT_PyOCL Program to enable image stack alignment in full-field X-ray absorption spectroscopy

SImPA SImPA(Simplified Imaging Plate Analysis / version 1.3) provides the necessary tools to process a powder X-ray diffraction image recorded on a phosphor imaging plate for further analysis as follows: (1) Image display and manipulation, e.g. pixel intensity readout, image enhancement and enlargement; (2) Sample-to-plate distance calibration for the analysis of the X-ray diffraction image; (3) Imaging plate orientation correction; (4) Removal of spurious high intensity spots (e.g. Bragg spots from large single grains); (5) Azimuthal summation of pixel intensities for the construction of a high signal-to-background intensity profile as a function of the diffraction angle. SImPA offers an easy-to-use interface. A working version of SImPA (version 1.3) is available free of charge for evaluation. Contact Serge Desgreniers (sdesgren@uOttawa.ca) for further information.

SIMPLEX Simulator and postprocessor for free-electron laser experiments

SIMPRO Full Powder Pattern Fitting Program. Refinement of multible phases, of the wave vector components of a modulated structures, Lorentz polarisation...

SIMREF Simultaneous Rietveld Refinement with Multible Powder Datasets.

SINGLE SINGLE can be used to control a variety of four-circle Eulerian-cradle single-crystal diffractometers including Hubers, the Stoe Stadi-4 and the Siemens P4.

Single Crystal To visualize the reciprocal lattice, simulate electron diffraction patterns and display stereographic projections. SingleCrystal reads from CrystalMaker binary files - or loads data directly from CrystalMaker via a menu command. Real-time manipulation and measurement is possible.

Single Crystal 4 SingleCrystal is a tool for understanding the diffraction properties of crystalline materials. Designed for physicists, chemists, material scientists and geologists, SingleCrystal 4 can simulate the results of tedious laboratory diffraction experiments - in real time, and from the comfort of your laptop. Observed electron diffraction images can also be analysed and their crystal orientations calculated - saving hours of painstaking measurement and analysis.

SIR2002 Ab initio resolution of macromolecular crystal structures.

SIR2011 The successor of SIR2004 and the latest program of the SIR suite.

SIR2014 the latest program of the SIR suite for crystal structure solution of small, medium and large structures. A variety of phasing algorithms have been implemented, both ab initio (standard or modern direct methods, Patterson techniques, Vive la Différence) and non-ab initio (simulated annealing, molecular replacement). The program contains tools for crystal structure refinement and for the study of three-dimensional electron-density maps via suitable viewers

Sir97

SIR97 Evolution of SIR92. Integrated package of computer programs for the solution and refinement of crystal structures using single crystal data.

SITCOM Facilitates the comparison of macromolecular substructures from different sources for validation purposes and to construct a consensus model containing sites from different substructures.

Situs Program package for the docking of protein crystal structures to single-molecule, low-resolution maps from electron microscopy. Developed to provide a robust and quantitative method for the localization of biomolecular subunits in low-resolution data. Use of single-molecule density maps that can be obtained by subtraction of maps from specimens of variable subunit composition. The central algorithm is a topology-representing neural network to correlate features within the structural data sets.

SizeCr The SizeCr software package designed to input and calculate the parameters of the material microstructure (crystallite size and microstrain in them) from the data of the XRD experiment for the XRD reflections of various types, Lorentzian (Lor), Gaussian (Gau), and pseudo-Voigt (pV). The SizeCr programm allows the calculation of points for construction of graphical techniques of Williamson-Hall plot (WHP) and Size-Strain plot (SSP).

SnB Based on Shake-and-Bake, a dual-space direct methods procedure for determining crystal structures from X-ray diffraction data.

SOWOS Program for the determination of the Wulff construction starting solely from the directions of the bounding facets.

SP2 A computer program for plotting stereographic projection and exploring crystallographic orientation relationships.

Space Group Explorer Gives you immediate access to much of the information which is available in the International Tables for Electron Crystallography, on-line in your own PC.

SPACER A program to display space-group information for a conventional and nonconventional coordinate system

Spartan

Spartan Student Edition is a serious molecular modeling package for teaching, and learning, chemistry. Combining Spartan's easy-to-use graphical interface with a targeted set of computational engines, the Student Edition provides fundamental molecular modeling utilities supporting the organic chemistry curriculum.

Spartan'14 offers all features and methods included in the Spartan Essential Edition, and in collaboration with Q-Chem, provides a full range of post-Hartree–Fock methods including density functional, Moller Plesset, thermochemistry recipes (including the new T1 procedure), and an assortment of advanced correlated approaches.

Spartan'14 Parallel Suite provides all the features of Spartan'14, but adds: multi-core parallel processing for ab initio, density functional, RI-MPT, and T1 calculations, the full SMD and SSPD data collections, and the ability to act as a compute server for other Spartan'14 licenses or the iSpartan molecular modeling app. The Spartan'14 Parallel Suite is the dominant version used in academic, government, and commercial research.

SPASM Tool for pattern recognition in protein structures at the level of assemblies of individual residues. See DEJAVU for the same at the level of fold.

SPE Space Group Explorer (SPE) for Windows. Gives you immediate access to much of the information which is available in the International Tables for Electron Crystallography, on-line in your own PC.

SPEC tools for acquiring, analyzing and plotting data

SPGR4D Computer program to derive (3 1)-dimensional symmetry operations from two-line symbols.

SR5 Rietveld program by Rod Hill and Ian Madsen (Ian.Madsen@csiro.au) of CSIRO Division of Minerals, Melbourne, Australia

SrRietveld SrRietveld extends and automates the popular existing Rietveld programs FullProf and GSAS to facilitate studies that involve many refinements, such as the analysis of large numbers of data sets. doi:10.1107/S0021889812045967/db5090sup1.zip (windows) doi:10.1107/S0021889812045967/db5090sup2.tar.gz (Linux, Unix or Mac)

SSM Interactive service for comparing protein structures in 3D. Allows for: comparison of two structures, examination of a structure for similarity with the whole PDB or SCOP archives, best Ca-alignment of compared structures, download and visualization of best-superposed structures using RasMol (Unix/Linux platforms) or RasTop (MS Windows machines), linking the results to other services - OCA, SCOP, GeneCensus, FSSP, 3Dee, CATH, PDBSum, SWISS-PROT and ProtoMap. SSM (Secondary Structure Matching) on homepage for PDBe Fold.

STAMP Alignment and analysis of protein 3-D structures.

STNET Drawing of Wulf nets. Part of the CCP4 suite

STOE IPDS Collection of software, from STOE, for measuring and evaluating intensities of twinned or grown-together crystals on the IPDS. Collection of images, multi-frames search, graphical representation, output (ShelX format)

STR3DI Molecular modeller for organic chemists. Allows measure of every geometric parameter, examination of each atom, bond, bond length, bond angle, torsional angle, and their accompanying stereo-electronic effects, in any organic molecule.

STRATEGY Program to aid in data collection strategy. You can run it after indexing the first frame using DENZO. Given the space group, it determines the spindle angle to start the data collection at.

StressTextureCalculator StressTextureCalculator (STeCa) is designed to facilitate fast, easy and automated access to area-detector data. Its outstanding features are direct calculation of diffraction patterns from different types of area-detector measurements, automatic data treatment and peak fitting using several implemented fit options. Software is available on request from the author.

Structure Tidy Puts crystal structures into standardized co-ordinates for comparison with other structures (to check if identical or isotypic). Available within Ton Spek's Platon (since Dec 2004). Parthe, E. & Gelato, L. M. (1984). Acta Cryst. A40, 169–183; Hu, S.-Z. & Parthe, E. (2004). Chin. J. Struct. Chem. 23, 1150–1160.

STRUVIR A STRUPLO to VRML converter. STRUVIR prepares .wrl

STRUVIR / STRUPLO for Windows STRUPLO for Windows is a MS-Windows version of STRUVIR, a program for producing polyhedra plots for inorganic crystal structures. It incorporates a Graphical User Interface (GUI) to make production of these plots much easier. Most of the commonly used features of STRUVIR are directly available from the GUI. The interface is similar to that of Ortep-3 for Windows, and loading a coordinate file will result in a default view of the structure immediately.

SUBGROUPGRAPH Analysis of group-subgroup relations between space groups. Available both as stand alone program or through a Web interface.

SUePDF SUePDF is a graphic-user-interface program written in MATLAB to achieve quantitative pair distribution functions (PDF) from electron diffraction data. The program facilitates the structural studies of amorphous materials and small nanoparticles based on electron diffraction data from transmission electron microscopes (TEM). SUePDF is distributed as free-to-use software.

Suites_for_small_molecules Review on suites of programs for small molecules

SUPERFLIP Solve crystal structures from diffraction data using the recently developed charge-flipping algorithm. It can solve periodic structures, incommensurately modulated structures and quasicrystals from X-ray and neutron diffraction data.

SURFNET Generates surfaces and void regions between surfaces from coordinate data supplied in a PDB file.

Swiss-PdbViewer Macintosh application that provides a user friendly interface allowing analysis of several proteins at the same time.

Symmet For the routine analysis of crystallographic texture by neutron diffraction at Chalk River Laboratories.

SYMMOL Symmetrizes a group of atoms whose coordinates, either orthogonal or oblique, are given in input. It prints out information about the given set of atoms and information concerning its symmetry: the symmetrized orthogonal coordinates together the point group (PG), the labels and the equivalent positions. Some quantities showing the goodness-of-fit are also printed: the rms on the coordinates, the molecular rms, the maximum deviation of the coordinates of the atom from the symmetrized ones and the continuous symmetry measure (CSM) for the whole PG and for the single elements of the PG.

SynchLink an iOS app for th front end to ISPyB, a laboratory information system for macromolecular crystallography synchrotron beamlines.