Crystallographic software list

MacMolecule Molecular graphics program used for displaying

MacPDF Search/Retrieval program for accessing the ICDD's PDF-2 Powder Diffraction database. MacPDF incorporated general Boolean Search, stick graph display and an interactive graphical phase identification facility. From Helios Software, Box 630 Norwich VT 05055 USA, phone +1-603-643-6009, fax +1-603-643-5337.

MacroModel Integrated software for Modeling Organic and

MacStripe Analysis pf protein sequences for alpha-helical coiled coils

MAG_sl Simulates x-ray resonant specular reflection from magnetic multilayers with account for interface roughness or transition layers. Magnetic scattering simulated by MAG_sl is due to resonant increase in the electric multipole part of x-ray scattering amplitude at the absorption edges of some rare-earth and transition elements. Can be used for characterization of magnetic multilayers.

MAIN

MAINDEX Manual indexation for area-detector crystallographic data.

MANTiS A program for the analysis of X-ray spectromicroscopy data (Multivariate ANalysis Tool for Spectromicroscopy)

MAP_CHANNELS a computation tool to aid in the visualization and characterization of solvent channels in macromolecular crystals

MapQTL Mapping of quantitative trait loci (QTLs).

MAPS Multiple Alignment of Protein Structures for comparisons of multiple protein structures. Can automatically superimpose the 3d models, detect which residues are structural equivalent and provide the residue-to-residue alignment, calculates a score of structure diversity, which can be used to build a phylogenetic tree.

MarchingCubeELD 3D and 2D electron density map visualization. Mainly focused on visualization of ELD calculated from X-ray diffraction data of small molecules, but it will work for small proteins as well.

MarchingCubes Generation of "3D" like Fourier electron density contour maps, for small molecule crystallography and powder diffraction

MarqX Modelling of powder diffraction data. Full documentation in line. Please note download to paolo.scardi@ing.unitn.it

MassEl The MassEL program allows to calculate masses of individual elements for synthesis of alloys, compounds or mixtures of specific compositions. For instance, in order to get 1 g of the FeSe compound you will have to mix 0.414 g of Fe and 0.586 g of Se. Mass of a specific element (e.g. you have 0.5 g of Fe for your synthesis) can be used as a reference as well.

MASSHA 3D graphic system to display and manipulate atomic structures and low resolution models.

Match Phase identification from X-ray powder diffraction data. Compares the user's diffraction pattern to the patterns stored in the ICDD PDF database.

MatInspector Detection of consensus matches in DNA sequences

MAUD MAUD stands for Material Analysis Using Diffraction. It is a general diffraction/reflectivity/fluorescence analysis program mainly based on the Rietveld method, but not limited to. The main features are: Written in Java can run on Windows, MacOSX, Linux, Unix (need Java VM 1.6 or later) Easy to use, every action is controlled by a GUI Works with X-ray, synchrotron, Neutron, TOF, electrons Developed for Rietveld analysis, simultaneous multi spectra and different instruments/techniques supported Ab-initio structure solution integration, from peak finding, indexing to solving Different optimization algorithms available (LS, Evolutionary, Simulated Annealing, Metadynamics) Le Bail fitting Quantitative phase analysis Microstructure analysis (size-strain, anisotropy and distributions included) Texture and residual stress analysis using part or full spectra MEEM and superflip algorithm for Electron Density Maps and fitting Thin film and multilayer aware; film thickness and absorption models Reflectivity fitting by different models, from Parratt (Matrix) to Discrete Born Approximation Works with TEM diffraction images and electron scattering Several data files input formats Works and input images from 2D detectors (image plates, CCD) CIF compliance for input/output; import structures from databases

MCE 2005 group of experimental program for 3D and 2D electron density map visualization. The software is mainly focused on visualization of ELD calculated from X-ray diffraction data of small molecules, but it will work for small proteins as well.

McMaille Indexing powder patterns by Monte Carlo and grid search.. The 2-theta peak positions extracted from a peak hunting program are used together with the intensities in order to build a pseudo powder pattern to which are compared patterns calculated from the cell parameters proposed by a Monte Carlo or by a grid systematic search process.

mcps Allows the automatic conversion of a section from an electron density map (in CCP4 format) to a ready-to-print postscript file containing a (dithered monochrome) grayscale representation of the electron density with a superimposed contour-line plot.

McStas Ongoing project to create a general tool for simulating neutron scattering instruments. The project is conducted at Ris 006e00610074ional laboratory as part of the RTD project.

MDBNCH A single run of MDBNCH performs seven independent molecular dynamics calculations, using systems of different sizes and/or using different codes. The purpose of doing this is to sample a variety of different running conditions. MDBNCH results provide information about the speed of machines in classical molecular dynamics calculations using short-range potentials and neighbor lists. More generally, they may give you a feeling about the behavior of systems on codes which are relatively small, but tend to access memory in a quite irregular way, probably causing many cache misses on recent RISC architectures.

MDComm Set of communications routines and programs which exchanges simulation data and interactive forces between NAMD and VMD.

Media Gallery Pro Media Gallery Pro, a goPro editor and MultiViewer capable of playing up to 6 HD movies simultaneously on a single display screen without additional hardware. Packed with robust features for audio visual editing, a powerful search functionality and movie/video indexing capabilities this is a must have software app that works well as a low end post production software suite. Media Gallery Pro also offers a full feature free 15 day trial available now. Edit your goPro movies, YouTube videos and more with this robust app for PC. Works great for creating sales presentations, trade show loops and point-of-sale scenarios for kiosks. Or, use as sports analysis tool capable of side by side movie and video playback for such things as perfecting golf swings. Download your copy and try MGP GoPro Editor/MultiViewer Video Player App. Or purchase the entire app for just $29.95USD and receive free updates for life.

Mercury Mercury offers a comprehensive range of tools for 3D structure visualization and the exploration of crystal packing. With a long pedigree and over 10,000 downloads, Mercury is firmly established as the visualiser of choice within the crystallographic community. With a vast number of options for customizing display settings Mercury is widely used for the generation of publication-quality images. A Style Manager contains a number of pre-defined display styles for work, publication and presentation and also provides the ability to preserve and share your own custom display settings. Stunning 3D images created using Mercury can be exported in a variety of common formats. In addition, it is possible to render high quality ray-traced images using POV-Ray.

MetLigDB MetLigDB is a publicly accessible web-based database through which the interactions between a variety of chelating groups and various central metal ions in the active site of metalloproteins can be explored in detail

Microcomputer cristallography Crystallographic Programs for Microcomputers

MicroED Electron diffraction of extremely small three-dimensional crystals (MicroED) allows for structure determination from crystals orders of magnitude smaller than those used for X-ray crystallography. The MicroED suite was developed to accomplish the tasks of unit-cell determination, indexing, background subtraction, intensity measurement and merging, resulting in data that can be carried forward to molecular replacement and structure determination.

MIMS Determination of structural parameters of incommensurate one-dimensionally modulated structures by an automatic search routine on four-dimensional Fourier maps.

MINCRYST Information-calculating system on crystal structure data of minerals. Includes structure Database for Minerals and formation of the Calculated Powder X-ray Diffraction Standards (CPDS) Subbase and X-ray powder diffraction analytical techniques and crystal chemical analysis. Exists as stand-alone package or Internet access (see bibliography).

MMCIF Macromolecular Crystallographic Information File

mmLib Python Macromolecular Library for the analysis and manipulation of macromolecular structural models

MMTK Program library for molecular modelling applications. Its aim is to provide researchers, especially those working on the development of new modelling methods, with a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular modelling.

Modeller Homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled and MODELLER automatically calculates a model containing all non-hydrogen atoms. Implements comparative protein structure modeling by satisfaction of spatial restraints and can perform many additional tasks, including de novo modeling of oligopeptides, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.

MODPLT Yamamoto's software for modulated structures

Modulated Structures software Problems and Solutions. Software for Incommensurate/Modulated Structures

MOE Molecular modelling from sequence analysis and alignment, multiple-structure alignment and superposition, remote homologue identification to 3D model building

MOIL-View Molecular modelling from sequence analysis and alignment, multiple-structure alignment and superposition, remote homologue identification to 3D model building

Molbridge For identifying nonbonded interactions in small molecules and biomolecular structures. The program is available in a standalone form and as an interactive web server with Jmol and JME incorporated into it.

MoleCoolQt MoleCoolQt is a molecule viewer designed for experimental charge density studies with a user-friendly graphical user interface.

Molecular graphics packages List of available software

Molecular Mass calculator With this program the mass of any molecule is easily calculated.

Molecular Studio from VisChem

Molecular Surface Molecular surfaces according to Conelly algorithm.

MOLGEN Automatic structure elucidation in chemistry:

MolIso Visualization of colour-mapped iso-surfaces from XD grid or GAUSSIAN CUBE files.

MOLMOL Display and analysis of macromolecular structures

Molphy Biology software mostly for Windows NT and DEC Alpha

MOLPLOT Powder programs of all sorts. Profile handling package

MolScat MolScat is an application that computes small-angle scattering intensities from user-provided three-dimensional models. The program can fit the theoretical scattering intensities to experimental X-ray scattering data.

MolScript Version 2.0. MolScript is a program for creating schematic or detailed molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures.

Molsee A Tcl/Tk-based program to control Rasmol

MolView Reads PDB, O plot files. Outputs QuickTime Movies, PICT (object oriented), DXF, and 3DMF files. Makes CPK, Ball&stick, Line, and ribbon drawings. The user can easily customize the diagram using a wide variety of colors and other display options on the whole or subsets of the molecule.Several examination tools are available:interactive Ramachandran, Edmunson wheel, hydropathy, distance, and B value graphs. The user can measure distances, find neighbors, display H bonds, Color by B values, Display by residue type, and a wide variety of other display options. This version also allows the user to display two different molecules and perform 3D least square alignments. The interface is entirely graphically oriented so the user does not have to memorize any line commands. The new 3D rendering output file (3DMF) supports the ribbon, ball&stick, stick, and CPK objects and can be read by 'MolView Lite' also found at this site. Cross-eye and wall-eye stereo is also supported. 'MOL' objects can be read in from 'O' plot files (e.g. electron density) or created in MolView and written out to separate files that can be read in at a later date. This allows 'lessons' to be created without using scripts. Emphasis is on the object-oriented, high resolution, 32bit color output rather than rotation speed.

MOMO MOMO is a Molecular Modelling program for organic molecules. It is parameterized for C, H, N, O, S, P, F, Cl, Br, I. We distribute a free test version (limited to 30 atoms, but with the full functionality). The full program version costs 400 DM for non-profit organizations and 4000 DM for industrial companies. This fee includes all further updates.

MOPRO Structure and Charge Density Refinement of Crystal Structures. It implements spherical and non spherical, multipolar model of atomic electron density, the latter being necessary to take into account the deformation of electron density arising from interatomic interactions, which becomes visible and quantifiable at subatomic resolution.

MOSFLM Integration of single crystal diffraction data from area detectors. Assumes that the experiment was conducted using the Arndt-Wonacott oscillation method, and also that monochromatic radiation was used.

MossA The program provides a straightforward approach to the fitting of ⁵⁷Fe conventional and synchrotron energy-domain Mössbauer spectra.

MPREP5 profil decomposition (part of CCP14)

MProbe Software tool for analyzing nonlinear

MPROFIL5 profil decomposition (part of CCP14)

MSG Web-based application to generate interactive, customizable views of molecular structures that can be displayed in a standard Web browser.

MSPcrunch Tools for improving database searching with Blast. First use

MulBlast MulBlast is small tool for rewriting of BLAST output file as multiple alignment file in MSF format. Easily compiled as an ANSI C program using either cc, gcc or c89 with any optimizer (O, O2, O3). The program is already compiled for HP-UX and IRIX running device and an exemple (luci_renre) is also provided.

MULTAN88 Structure resolution. Version from Molecular Structure Corporation

MultiSimplex MultiSimplex is a software for sequential experimental design and optimization, based on the simplex algorithms and fuzzy set membership functions. MultiSimplex is used to optimize scientific instruments in analytical chemistry and related disciplines . Succesful applications both in research and production. Description, manual and demo versions are available at the web site. Academic discount.

MuPad A parallel and general purpose computer algebra system

MxCuBE MxCuBE allows users to easily and simply interact with beamline hardware components and provides automated routines for common tasks in the operation of an ESRF synchrotron beamline at dedicated to experiments in MX.

MxDC and MxLIVE Software for data acquisition, information management and remote access to macromolecular crystallography (MX) beamlines at the Canadian Light Source (CLS)