Crystallographic software list

DADIMODO Program for refining atomic models of multidomain proteins or complexes against small-angle X-ray scattering data. Interdomain distance and orientational restraints, such as those derived from NMR measurements, can be included in the optimization process. A software package including the Python code, documentation, examples and additional scripts is available from the authors on request.

DAJUST DAJUST is the generic name of a software package for powder diffraction formed by the core programs AJUST and SGAID. AJUST performs whole-pattern matching (cell-parameter refinement, profile fitting and intensity extraction), SGAID provides a list of the most probable space groups.

Dans_Diffraction Python package that reads crystal structures from CIFs and simulates diffraction patterns. Data are included for calculation of x-ray and neutron structure factors. Single crystal and powder plots can be generated quickly and easily by either a basic GUI or a command line approach. On the command line, a crystal Object is created with structure properties imported from the CIF, which are editable. The object has many useful attributes including plotting and scattering simulations. Dans_Diffraction is available from PyPi: pip install Dans_Diffraction or Github: git clone https://github.com/DanPorter/Dans_Diffraction.git

Dans_Diffraction Dans_Diffraction is package to read cif files and simulate diffraction patterns, among other things.

DASH User-friendly graphical-user-interface-driven computer program for solving crystal structures from X-ray powder diffraction data, optimized for molecular structures.

Data Analysis WorkbeNch (DAWN) The Data Analysis WorkbeNch (DAWN) was developed to address the challenge of providing a single visualization and analysis platform for data from any synchrotron experiment (including single-crystal and powder diffraction, tomography and spectroscopy), whilst also being sufficiently extensible for new specific use case analysis environments to be incorporated (e.g. ARPES, PEEM)

DATARED For the data reduction. Single crystal data reduction program. Corrects Lp, absorption and background intensities. Applicable to any system. To single crystal spheres. Converts the uncorrected structure factors into Lp, absorption and background corrected structure factors. See also dremablp. Exists as a GUI version named dataredwin.

DATAREDWIN Similar to the program dremablp (program 7). If the input is in the form of - left background intensity - peak intensity - right background intensity, you can use this program for the data reduction. Single crystal data reduction program. Corrects Lp, absorption and background intensities. Applicable to any system. To single crystal spheres. Converts the uncorrected structure factors into Lp, absorption and background corrected structure factors.

Datasqueeze graphical interface for analyzing data from 2D x-ray detectors (image plate, CCD, wire). Facilities for pixel-by-pixel examination of the raw data, re-centering and calibrating the image, correcting for detector tilt relative to the incident beam, producing x-y plots of intensity versus Q (the momentum transfer), 2-theta, Qx, Qy, chi, as a Porod or Guinier plot, or along an arbitrary line across the image. Useful for the analysis of powder diffraction data, diffuse scattering from polymers or liquid crystals, or small-angle scattering from colloids, polymers, gels, or solutions. Not well suited for extracting intensities from many sharp Bragg peaks in a single-crystal diffraction type experiment

DataThief Program to reverse engineer scanned graphs to datapoints.

DATCOR Semi-empirical absorption correction (North algorithm). Input azimuthal data with psi angles. Many novel smoothing and data display routines. Program by JH Reibenspies at Texas A&M.

DATSEE companion program for the then

DBWatcher Sequence analysis batch software

DBWS Tools Graphical interface for DBWS, program for Rietveld refinements. Handles refinement jobs by compiling Input Control Files (ICF's) for DBWS, importing the CIF files from ICSD, running the program and showing the graphical results using the shareware program DMPlot, which plots diffraction patterns. For original programs see: http://www.ccp14.ac.uk/ccp/web-mirrors/dbws/downloads/young/download_dbws.html

DDMP Difference distance matrix plot.

DEBUSSY DebUsSy stands for Debye User System and consists of a suite of programs implementing a fast approach to the Debye Scattering Equation (DSE) Analysis for powder diffraction data from nanocrystalline and/or non-ordered materials. Debussy uses the previously created database(s) and carries out a fast calculation of the diffraction profile of each cluster that contributes to the total pattern, according to a suitable and adjustable size-distribution function. The analysis can be performed on single- or multiple-phase specimens, trying to fit one or more experimental data sets collected with Synchrotron or laboratory X-ray, neutron and electron beams. For all radiation types, the scattering amplitudes/factors of atomic species are encoded into the program. Different options are also available to deal with lattice expansions or contractions variable with the crystal size. Both Chebyshev polynomials and experimentally collected data can be used to manage the background component.

DEBVIN Rietveld refinment with generalized coordinates subjected to geometrical constraints.

DebyeFit DebyeFit is a tool to calculate the Debye or Einstein characteristic temperature of thermal vibrations in crystals from the equivalent atomic displacement parameters (ADPs) of any atom at user’s option that have been obtained at several temperatures. The ADP values are separated into static and dynamic components to get a best fit to the model Debye / Einstein curve. Calculations are based on the Debye, Einstein or mixed model at user’s option. An additional term is first added to the equations to account a possible static disorder. Nonlinear least-square technique is used to refine parameters of the model curve for the set of ADPs observed in the various-temperature structural study. The program provides a good fit up to 0.5 – 2% between the theoretical and observed ADP values. It is quite possible that the best dependence is first achieved within the framework of the Debye or Einstein models between ADPs obtained at different temperatures owing to a simple modification of the formalism

DEF4 Simulation of plane wave topographs for dislocations

DEFW Simulation of section topographs for dislocations

DEJAVU To recognize arrangements of secondary structure elements.

DEMON Protein program suite. Name short for density modification.

DENFERT An algorithm for improvement of the ab initio restoration of biomacromolecular structure from small-angle X-ray scattering data, by consideration of an additional type of `dummy atom', representing the hydration layer is implemented in the program DENFERT.

DENSS DENSS is an algorithm that reconstructs the 3D density of a molecule from the 1D solution scattering (SAXS) profile using a novel iterative phase retrieval procedure. DENSS takes as input the 1D scattering data and outputs a standard MRC formatted density map. Several tools and scripts are included for performing data analysis, calculation of the pair distribution function and particle size estimates, averaging of multiple MRC maps, and alignment of PDB atomic models to density maps. An online web server called DENSSWeb is also available at denss.ccr.buffalo.edu.

DENZO DENZO is the integration component of a set of programs, HKL, authored by Wladek Minor and Zbyszek Otwinowski.

DetOx A program for determining anomalous scattering factors of mixed-oxidation-state species

DEXA Differential EXAFS is a new XAS technique dedicated to directly measuring the tiny atomic displacements that arise from such strain-inducing phenomena as magnetostriction, piezoelectricity and thermal expansion. These new experiments have presented the need for new analysis tools to extract and quantify the measured atomic strains, a need that has been addressed by the development of the DEXA code.

Diamond For Diamond structures program to refine parameters in the harmonic approximation. refines individual thermal, scale, extinction parameters in diamond type structures.

DIAMOND Visual crystal structure information system for molecular and solid state chemists as well as for surface and material scientists.

DICVOL91 part of the CCP14 suite. Indexing program

DIFABS PC version of the program by N.Walker with test files.

DIFFaX Calculates diffraction patterns from crystals that contain coherent planar defects, such as twins and stacking faults. Computes the average wave function from each layer occured in a faulted crystal and the incoherent intensity contribution

DIFFRACplus TOPAS Graphics based profile analysis program integrating various types of X-ray and neutron diffraction analyses by supporting all profile fit methods currently employed in powder diffractometry

Diffraction Pattern Calculator (DPC) a toolkit for a user-friendly approach to unit-cell lattice parameter identification of two-dimensional grazing-incidence wide-angle X-ray scattering data. The code for this program was written in MATLAB.

DiffractWD Program for basic powder pattern manipulations and visualization. It provides a user-friendly interface for comparison of spectra with each other and with simulated patterns based on single-crystal data.

DIMS direct-method program for solving incommensurate modulated structures and composite structures. The result of this program can be automatically interpreted by the program MIMS to obtain a 4D-structure model ( 4D-modeling in VEC).

DIRDIF Computer program system for crystal structure determination by Patterson methods and direct methods applied to difference structure factors. Dirdif 99.2 enhancements over Dirdif 96 is that it is more powerful and can handle significant deviations from the correct cell contents.

DISCUS Modelling, Materials Science, Scattering, Teaching. Description: Diffuse Scattering and Defect-structure simulation. Simulates crystal structures and to calculate the corresponding Fourier transform.

DLS-76 Simulation of crystal structures by geometric refinement.

DOCK Docking of molecules.

DOMAK Program to define domains in protein 3D structures.

DPDAK software for simple and fast on- and offline reduction and analysis of X-ray scattering data. It is an open-source software with a plug-in structure allowing tailored extensions.

DPLOT 2D Graphing Utility

DPS Complete package for data processing of crystallographic area detector data. Special features will be a transparent networking environment with a Web-based graphical user interface and parallized code for the most time consuming computational methods.

DRAGON DRAGON is a protein modelling tool using Distance Geometry. DRAGON attempts to predict the tertiary structure of a smallDRAGON communicates with you through a simple command-line interface which is used to specify parameter values and input filenames. soluble protein, given its sequence, the secondary structure and possibly a set of interresidue distance restraints.

DRAW The best and fastest way to get HPGL files into WORD 6 documents.

DRAWHCA HCA drawing directly through the Web from amino-acids sequences

DRAWxtl Display of crystal structures (ball-and-stick, polyhedra, thermal ellipsoids). Can import data in Shelx, Gsas, Cif and CSD fdat format. Produces output files in the Virtual Reality Modelling Language (VRML) or Persistence of Vision (POV-RAY) ray-tracing formats. The VRML format can be viewed locally or across the Internet, and the viewer can rotate and/or zoom the drawing in real time. Beginning with V2.4, the user can generate either VRML V1.0 or VRML97 (V2.0) format. In the latter form, it is possible to animate drawings as shown in the 'wrl' files included in the distribution.

DREMABLP Single crystal data reduction program. Corrects Lp, absorption and background. Applicable to any system. To single crystal spheres. Exists as a GUI version named dremablpwin. Converts the uncorrected structure factors into Lp and absorption corrected structure factors.

DREMABLP For the data reduction. Single crystal data reduction program. Corrects Lp, and absorption. Applicable to any system. To single crystal spheres. Converts the uncorrected structure factors into Lp and absorption corrected structure factors.

DREMABLPWIN For the data reduction. Single crystal data reduction program. Corrects Lp, and absorption. Applicable to any system. To single crystal spheres. Converts the uncorrected structure factors into Lp and absorption corrected structure factors.

DRXWin Graphical and Analytical Tools for XRD Powder Patterns. Let you work with X-Ray diffraction files coming from several diffractometers (Siemens, Philips, Rigaku, Stoe, Seifert, etc.), and Rietveld programs like FullProf and RIET7.

DS 4-circle Diffractometer Simulation

dSNAP to help users automatically classify and visualise the results of database searches using the Cambridge Structural Database.

DSR - Disordered Structure Refinement Its main purpose is the transfer of molecular fragments to a user-defined location in the target structure. Writing a special DSR command into the SHELXL .res file of the target structure instructs DSR on where to place and how to orient a molecular fragment from the fragment database in the unit cell. In addition, it is possible to define the occupancy, residue or part number of the inserted fragment. The fragment can be inverted, e.g. to fit the second conformer of twisted tetrahydrofuran. If desired, automatically calculated distance restraints for all bonds in the molecular fragment can replace the restraints obtained from the database. Additional options in the system command line allow the import and export of molecular fragments to and from the database, and listing of and searching for database content.

DXAS Calibration DXAS Calibration provides a quantitative and automated solution to the problem of calibrating spectra from dispersive XAS beamlines.

dxtbx toolbox The dxtbx software package provides a consistent interface to both image data and experimental models, while supporting a completely generic user-extensible approach to reading the data files.