Entered: Mon Nov 17 16:38:02 DFT 2003
Operating systems: Windows.
Type: Binary.
Languages: C++.
Distribution: Commercial
Application fields: Chemistry, Structure, Mineralogy, Powder.
Description: Phase identification from X-ray powder diffraction data. Compares the user's diffraction pattern to those stored in the ICDD PDF2 database in order to identify the phases.
References: http://www.crystalimpact.com/match/index.html

MCE

Entered: Thu Feb 26 10:38:02 DFT 2004
Operating systems: Windows, Linux.
Type: Binary.
Distribution: Free
Application fields: Structure, Electron Microscopy.
Description: 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.
References: http://www.ccp14.ac.uk/ccp/web-mirrors/marchingcube-fourierviewer/~husakm/Public/MarchingCubeELD/MarchingCubeELD.htm

MDBNCH

Entered: Wed Jun 18 12:38:02 DFT 1997
Operating systems: Unix, MacOS, Windows, VMS, .
Type: Source.
Languages: Fortran.
Distribution: Free
Application fields: Biology, Chemistry, Structure.
Description: 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.
References: http://www.sissa.it/furio/Mdbnch/info.html

MDComm

Entered: Mon Oct 19 8:52:34 DFT 1998
Operating systems: Unix.
Languages: C++.
Distribution: Free
Application fields: Biology.
Bibliography: Comput. Phys. Commun., 91:111--134, 1995.
Description: Set of communications routines and programs which exchanges simulation data and interactive forces between NAMD and VMD.
References: http://www.ks.uiuc.edu/Research/mdscope/#mdcomm

MIMS

Entered: Fri Oct 22 9:11:16 DFT 1999
Operating systems: Unix.
Languages: Fortran.
Distribution: Free
Application fields: Materials Science, Structure determination.
Bibliography: J. Appl.Cryst.(1999) 32,5, 1017-1020
Description: Determination of structural parameters of incommensurate one-dimensionally modulated structures by an automatic search routine on four-dimensional Fourier maps.
References: mailto:fan@aphy.iphy.ac.cn

MINCRYST

Entered: Mon Oct 11 10:41:18 DFT 1999
Operating systems: Windows, .
Type: Binary.
Languages: Delphi, Paradox.
Application fields: Minerals.
Bibliography: http://database.iem.ac.ru./mincryst/.
Description: 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).
References: http://database.iem.ac.ru/mincryst/descript.htm

MMCIF

Entered: Fri Nov 22 8:27:54 NFT 1996
Operating systems: Windows, VMS, Unix.
Distribution: Free
Application fields: Chemistry, Biology, Structure determination.
Description: Macromolecular Crystallographic Information File
References: mmCIF

MMTK

Entered: Fri Mar 20 15:57:15 NFT 1998
Operating systems: Unix, MacOS, Windows.
Languages: Python.
Application fields: Biology.
Description: 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.
References: http://starship.skyport.net/crew/hinsen/mmtk.html

MODPLT

Entered: Mon Jan 6 13:15:59 NFT 1997
Operating systems: .
Application fields: Materials Science, Structure determination.
Description: Yamamoto's software for modulated structures
References: Wellcome to the Superspace

MOE

Entered: Thu Mar 30 10:16:36 DFT 2000
Operating systems: Unix.
Type: Binary.
Distribution: Commercial
Application fields: Biology, Graphics, visualization, virtual reality.
Description: Molecular modelling from sequence analysis and alignment, multiple-structure alignment and superposition, remote homologue identification to 3D model building
References: http://www.chemcomp.com/

MOIL-View

Entered: Wed Dec 4 16:46:04 NFT 1996
Operating systems: Unix, Irix, AIX.
Application fields: Biology.
Description: Program for Visualization of Structure and
References: ftp://munin.ucsf.edu/pub/

MOLGEN

Entered: Wed Dec 4 16:46:04 NFT 1996
Operating systems: Unix, VMS, Windows.
Distribution: Free
Application fields: Biology, Chemistry.
Description: Automatic structure elucidation in chemistry:
References: MOLGEN structure generation

MOLMOL

Entered: Thu Oct 30 8:38:32 NFT 1997
Operating systems: Unix, Irix, AIX, OSF1, Linux.
Type: Source, Binary.
Distribution: Free
Application fields: Graphics, visualization, virtual reality.
Description: Display and analysis of macromolecular structures
References: http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

MOLPLOT

Entered: Wed Dec 4 16:46:53 NFT 1996
Operating systems: Windows.
Distribution: Free
Application fields: Chemistry, Minerals, Powder, Chemistry.
Description: Powder programs of all sorts. Profile handling package (part of
References: CCP14 Program Suite

MOMO

Entered: Thu Feb 20 19:07:20 NFT 1997
Operating systems: Windows, .
Type: Binary.
Languages: Fortran.
Distribution: Commercial
Application fields: Modelling.
Description: 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.
References: MOMO -- Homepage

MOPRO

Entered: Tue Aug 29 16:36:49 DFT 2006
Operating systems: Linux, Windows, MacOS, Dec Alpha.
Type: Binary.
Languages: Fortran, Java.
Distribution: Free Academic
Application fields: Biology, Chemistry, Modelling, Structures.
Bibliography: Jelsch, C., Guillot, B., Lagoutte, A. & Lecomte, C., (2005). J. Appl. Cryst. 38, 38-54.<BR>

Guillot B., Viry L., Guillot R., Lecomte C. & Jelsch C. (2001) J. Appl. Crystal. 34, 214-223.
Description: 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.
References: http://www.emqc.uhp-nancy.fr/mopro.html

MOSFLM

Entered: Thu Apr 3 10:46:55 NFT 2003
Distribution: Free
Type: Binary
Systems: Linux, MacOS
Distribution: Free
Application fields: Biology.
Description: 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.
References: http://www.mrc-lmb.cam.ac.uk/harry/mosflm/

MPREP5

Entered: Wed Dec 4 16:46:55 NFT 1996
Distribution: Free
Application fields: Chemistry, Minerals, Powder.
Description: profil decomposition (part of CCP14)
References: CCP14 Program Suite

MPROFIL5

Entered: Wed Dec 4 16:46:55 NFT 1996
Distribution: Free
Application fields: Chemistry, Minerals, Powder.
Description: profil decomposition (part of CCP14)
References: CCP14 Program Suite

MProbe

Entered: Mon Jan 6 13:33:49 NFT 1997
Operating systems: Windows.
Distribution: Free
Application fields: Mathematics.
Description: Software tool for analyzing nonlinear
References: MProbe

MSG

Entered: Fri Oct 22 9:17:07 DFT 1999
Operating systems: Unix, MacOS, Windows, VMS, .
Type: Source.
Languages: Perl, VRML.
Distribution: Free
Application fields: Biology, Graphics, visualization, virtual reality.
Bibliography: J.Appl.Cryst. (1999)32,5, 1026-1027
Description: Web-based application to generate interactive, customizable views of molecular structures that can be displayed in a standard Web browser.
References: http://mice.sdsc.edu/msg/

MSPcrunch

Entered: Fri Feb 21 19:14:36 NFT 1997
Operating systems: Unix, VMS.
Type: Source, Binary.
Distribution: Free
Application fields: Biology.
Description: Tools for improving database searching with Blast. First use
References: ftp://ftp.sanger.ac.uk/pub/HSPcrunch/

MULTAN88

Entered: Wed Dec 4 16:46:55 NFT 1996
Distribution: Commercial
Application fields: Chemistry, Structure determination.
Description: Structure resolution. Version from Molecular Structure Corporation
References: Molecular Structure Corporation Home Page

MacMolecule

Entered: Fri Mar 7 20:01:29 NFT 1997
Operating systems: MacOS.
Type: .
Distribution: Free
Application fields: Graphics, visualization, virtual reality, Biology.
Description: Molecular graphics program used for displaying
References: PCMolecule2 and MacMolecule2 Molecular Graphics Software

MacPDF

Entered: Wed Jul 15 9:04:03 DFT 1998
Operating systems: MacOS.
Type: Binary.
Languages: C.
Distribution: Commercial
Application fields: Databases, Diffraction.
Description: 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.
References: mailto:Richard.Rose@valley.net

MacStripe

Entered: Fri Nov 22 8:27:48 NFT 1996
Operating systems: MacOS.
Distribution: Free
Description: Analysis pf protein sequences for alpha-helical
References: Coiled Coils

MacroModel

Entered: Fri Nov 22 8:27:48 NFT 1996
Operating systems: Unix.
Application fields: Biology.
Description: Integrated software for Modeling Organic and
References: MacroModel Home Page

MapQTL

Entered: Tue Jan 7 11:18:57 NFT 1997
Operating systems: Windows, MacOS, VMS, Solaris.
Distribution: Commercial
Application fields: Biology.
Description: Mapping of quantitative trait loci (QTLs).
References: Genetic Mapping Software of CPRO-DLO

MarchingCubeELD

Entered: Mon Feb 28 9:00:40 NFT 2000
Operating systems: Windows.
Type: Binary.
Languages: C++, Visual Basic .
Distribution: Free
Application fields: Graphics, visualization, virtual reality, Modelling, Structure determination, Teaching.
Description: 3D and 2D electron density visualization program based on HW OpenGL accelerated graphic. Can be used together with CRYSTALS structure determination package or SHELX via the WinGX interface. Works with stereoscopic displays and devices.
References: http://mysak.umbr.cas.cz/~husakm/Public/MarchingCubeELD/MarchingCubeELD.htm

MarchingCubes

Entered: Wed Jul 14 18:09:27 DFT 1999
Operating systems: Windows.
Type: Binary.
Distribution: Free
Application fields: Powder, Structure.
Description: generation of "3D" like fourier electron density contour maps, for small molecule crystallography and powder diffraction
References: http://www.ccp14.ac.uk/tutorial/marchingcube/

Marching Cube ELD

Entered: Thu Apr 3 10:32:34 NFT 2003
Operating systems: Windows, Linux.
Type: Binary.
Distribution: Free
Application fields: Visualization, structure determination, biology.
Description: 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.
References: http://www.ccp14.ac.uk/ccp/web-mirrors/marchingcube-fourierviewer/~husakm/Public/MarchingCubeELD/MarchingCubeELD.htm >

MarqX

Entered: Wed Feb 23 18:32:34 NFT 2000
Operating systems: Windows.
Type: Binary.
Languages: Fortran.
Distribution: Free
Application fields: Diffraction.
Bibliography: YH Dong and P Scardi J. Appl. Cryst. 33 (2000) 184-189
Description: Modeling of powder diffraction data. Full documentation in line. Please notify download to :Paolo.Scardi@ing.unitn.it
References: ftp://MarqX:release@bragg.ing.unitn.it

Match

Entered: Thu Apr 3 10:27:53 NFT 2003
Operating systems: Windows
Type: Binary.
Application fields: Powder, mineralogy
Description: Phase identification from X-ray powder diffraction data. Compares the user's diffraction pattern to the patterns stored in the ICDD PDF database.
References: http://www.crystalimpact.com/match/

MatInspector

Entered: Fri Nov 22 8:27:53 NFT 1996
Operating systems: Unix, VMS, Windows, MacOS.
Application fields: Biology.
Description: Detection of consensus matches in DNA sequences
References: AG BIODV: Software Development for Molecular Biology

McMaille

Entered We Oct 30 11:58:00 NFT 2002
Operating systems: Windows
Type: Binary, Source.
Languages: Fortran
Distribution: Free
Application fields: Powder, Mineralogy
Description: 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.
References: http://www.cristal.org/McMaille/

mcps

Entered: Tue Mar 13 16:38:17 NFT 2001
Operating systems: Irix, Solaris, OSF1, Linux.
Type: Binary.
Languages: C.
Distribution: Free
Application fields: Biology, Electron microscopy, Graphics, visualization, virtual reality.
Description: 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

Entered: Tue Sep 7 15:25:09 DFT 1999
Operating systems: Unix, HPUX, OSF1, Linux.
Type: Source, Binary.
Languages: C.
Distribution: Free academic
Application fields: Instrumentation, Neutron.
Bibliography: K. Lefmann, K. Nielsen Neutron News, Vol 10, 3, 1999
Description: Ongoing project to create a general tool for simulating neutron scattering instruments. The project is conducted at Risø national laboratory as part of the RTD project.
References: http://neutron.risoe.dk/mcstas/

Microcomputer cristallography

Entered: Fri Nov 15 17:38:42 NFT 1996
Operating systems: Windows, MacOS.
Description: Crystallographic Programs for Microcomputers
References: /sincris-top/logiciel/prg-micro.html

mmLib

Entered: Thu Feb 26 17:38:42 NFT 2004
Operating systems: Linux.
Language: Python Type: Source.
Application fields: Biology.
Distribution: Free
Bibliography: JAC 37,1, 174-178 (2004) Description: Python Macromolecular Library for the analysis and manipulation of macromolecular structural models
References: http://pymmlib.sourceforge.net/

Modeller

Entered: Mon Jan 21 10:20:52 NFT 2002
Operating systems: Irix, AIX, Solaris, OSF1, Linux.
Type: Binary.
Languages: Fortran.
Distribution: Free academic
Application fields: Biology.
Description: 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.
References: http://tatiana.rockefeller.edu/modeller/

Modulated Structures software

Entered: Tue Mar 31 15:25:28 DFT 1998
Operating systems: Unix, Windows, VMS.
Type: Source.
Distribution: Free
Application fields: Powder.
Description: Problems and Solutions. Software for Incommensurate/Modulated Structures
References: http://www.dl.ac.uk/CCP/CCP14/solution/incomm.htm

MolIso

Entered: Thu Dec 28 15:25:28 DFT 2006
Operating systems: Linux, Windows.
Source: C
Type: Binary, Source.
Distribution: Free
Application fields: structure, visualization
Bibliography: JAC (2006) 39, 6, 901
Description: Visualization of colour-mapped iso-surfaces from XD grid or GAUSSIAN CUBE files.
References:http://userpage.chemie.fu-berlin.de/~chuebsch/moliso/

MolScript

Entered: Mon Jan 5 9:00:38 NFT 1998
Operating systems: Unix.
Type: Source.
Languages: C.
Distribution: Free academic
Application fields: Biology.
Description: 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.
References: http://www.avatar.se/molscript/

MolView

Entered: Mon Mar 10 12:56:02 NFT 1997
Operating systems: MacOS.
Type: Binary.
Languages: C.
Distribution: Free
Application fields: Graphics, visualization, virtual reality.
Description: 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.
References: http://bilbo.bio.purdue.edu/~tom

Molecular Studio

Entered: Wed Dec 4 16:46:04 NFT 1996
Operating systems: .
Application fields: Chemistry, Biology.
Description: from VisChem
References: ftp://ftp.cs.orst.edu/pub/next/demos/science/VisChemMoleculeStudio.README

Molecular Surface

Entered: Wed Dec 4 16:46:04 NFT 1996
Operating systems: .
Application fields: Biology.
Description: Molecular surfaces according to Conelly algorithm. Available from
References: mailto:qcpe@ucs.indiana.edu

Molecular graphics packages

Entered: Wed Dec 4 16:46:04 NFT 1996
Operating systems: .
Distribution: Free academic
Application fields: Graphics, visualization, virtual reality, Biology.
Description: List of available software
References: ftp://infomeister.osc.edu/pub/chemistry/documents/molecular_graphics_packages

Molecular Mass calculator

Entered: Mon Feb 1 10:20:17 NFT 1999
Operating systems: Windows.
Type: Binary.
Distribution: Free
Application fields: Biology.
Description: ith this program the mass of any molecule is easily calculated.
References: http://home.wxs.nl/~pvsanten/mmp/main.htm

Molphy

Entered: Wed Dec 4 16:46:32 NFT 1996
Operating systems: Windows, VMS.
Distribution: Free
Application fields: Biology.
Description: Biology software mostly for Windows NT and DEC Alpha
References: Biology Software for Alpha NT

Molsee

Entered: Tue Mar 13 17:07:28 NFT 2001
Operating systems: Unix.
Type: Source.
Languages: TCl/Tk.
Distribution: Free academic
Application fields: Graphics, visualization, virtual reality.
Bibliography: J. Appl. Cryst. (2000)33,6,1445
Description: A Tcl/Tk-based program to control Rasmol
References: http://mdl.ipc.pku.edu.cn/software/molsee.html

MuPad

Entered: Mon Jan 6 13:34:15 NFT 1997
Operating systems: Unix, Windows, MacOS.
Distribution: Free
Application fields: Mathematics.
Description: A parallel and general purpose computer algebra system
References: MuPAD - Home Page

MulBlast

Entered: Thu Mar 27 12:13:33 NFT 1997
Operating systems: Unix, HPUX, Irix.
Type: Source, Binary.
Languages: C.
Distribution: Free
Application fields: Biology.
Description: 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.
References: ftp://ftp.lmcp.jussieu.fr/pub/sincris/software/protein/

MultiSimplex

Entered: Thu Jan 14 8:47:25 NFT 1999
Operating systems: Windows.
Type: Binary.
Languages: VB and VBA.
Distribution: Commercial
Application fields: Chemistry.
Description: 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.
References: http://www.multisimplex.com

N [top]

NAB

Entered: Wed Dec 4 16:46:57 NFT 1996
Operating systems: Unix.
Application fields: Biology.
Description: Manipulation language for modelling of nucleic acids.
References: ftp://ftp.scripps.edu/pub/macke/

NAG

Entered: Mon Jan 6 13:34:47 NFT 1997
Operating systems: Unix, VMS.
Distribution: Commercial
Application fields: Mathematics.
Description: Numerical software libraries
References: The Numerical Algorithms Group Ltd

NAMD

Entered: Mon Oct 19 8:44:20 DFT 1998
Operating systems: Unix, HPUX, Irix, Solaris, Linux, .
Distribution: Free
Application fields: Biology.
Description: Parallel, object-oriented molecular dynamics program designed for high performance molecular dynamics simulations of large biomolecular systems.
References: http://www.ks.uiuc.edu/Research/namd/

NAOMI

Entered: Wed Dec 4 16:47:10 NFT 1996
Operating systems: Irix.
Application fields: Biology.
Description: for use in studying three-dimensional protein structures
References: /sincris-top/logiciel/prg-naomi.html

NBS*QUANT85

Entered: Wed Dec 4 16:47:10 NFT 1996
Distribution: Free
Application fields: Chemistry, Minerals, Powder.
Description: Quantitative analysis (part of CCP14)
References: CCP14 Program Suite

NCEMSS

Entered: Fri Mar 6 9:25:45 NFT 1998
Operating systems: Irix, AIX, Solaris, OSF1, VMS.
Distribution: Free
Application fields: Electron microscopy.
Description: HRTEM images based on the multislice approximation. The program is quite flexible and supports input of structures, viewing of unit cells, calculation of images and diffraction patterns, various layout options.
References: http://ncem.lbl.gov/NCEM/computer/software.html

NEUTRON

Entered: Mon Mar 8 13:25:45 NFT 2004
Operating systems: Web.
Distribution: Free
Application fields: Neutron Diffraction.
Bibliography: J.Appl.Cryst. (2004), 36,4, 1085-1089
Description: calculates systematic absences in inelastic neutron scattering spectra, due to the phonon symetry.
References: http://www.cryst.ehu.es/rep/neutron.html

NMR

Entered: Wed Dec 4 16:47:14 NFT 1996
Operating systems: .
Application fields: Teaching.
Description: NMR Educational software
References: http://www.chem.umu.se/divisions/fk/EduNMRSoft.html

NMRFIT

Entered: Wed Dec 4 16:47:14 NFT 1996
Operating systems: .
Application fields: Minerals, Materials Science.
Description: Simulation of short-range Al/Si order in framework
References: NMRFIT: Program to obtain Al/Si order from NMR data

NOC

Entered: Mon Apr 11 8:43:50 NFT 2005
Operating systems: Windows.
Type: Binary.
Distribution: Free
Application fields: Proteins
Description: For protein structure model-building, visualization, validation and analysis ... Auto-fit residues' side-chain against density data (experimental function) - Solid surface creating and electrostatic potential, hydrophobic force coloring - Hardware stereo view supported - Side by side stereo view
References: http://noc.ibp.ac.cn/

NOCHAOS

Entered: Fri Nov 7 8:43:50 NFT 1997
Operating systems: Windows.
Type: Source, Binary.
Languages: Fortran, C.
Distribution: Free
Application fields: Minerals, Powder, Structure.
Description: A program for fast building of distance-constrained starting configuration files for RMCA modelling.
References: http://fluo.univ-lemans.fr:8001/glasses/rmca/nochaos.html

NOPT

Entered: Wed Dec 4 16:47:10 NFT 1996
Operating systems: .
Distribution: Free
Application fields: Biology, Materials Science.
Bibliography: http://www.iucr.org/journals/jac
Description: Program for optical-activity calculations.
References: mailto:mucha@trurl.ch.uj.edu.pl

NUCPLOT

Entered: Fri Jan 23 16:02:11 NFT 1998
Operating systems: Unix, Irix, Windows, Linux, .
Type: Source.
Languages: C.
Distribution: Free academic
Application fields: Biology, Structure, Structure determination.
Bibliography: Nucleic Acids Research, 25, 4940-4945.
Description: NUCPLOT is a program which generates schematic diagrams of protein-nucleic acid interactions. The program automatically identifies these interactions from the 3D atomic coordinates of the complex from a PDB file and generate a plot that shows them in a clear and simple manner.
References: http://www.biochem.ucl.ac.uk/~nick/nucplot.html

NeXus

Entered: Fri Oct 22 8:46:48 DFT 1999
Operating systems: Unix, VMS, .
Type: Source.
Languages: Fortran, C.
Distribution: Free
Application fields: Diffraction, Materials Science, Powder, Structure.
Description: API which works with the NeXus Data Definition Language. Nexus is a portable data exchange format for neutron and X--ray scattering.
References: ftp://hydra.pns.anl.gov/pub/NeXus/

NetSci

Entered: Mon Jan 6 13:41:43 NFT 1997
Operating systems: .
Application fields: .
Description: Network Science software listings
References: The NetSci Homepage

Netlib

Entered: Mon Jan 6 13:35:06 NFT 1997
Operating systems: .
Distribution: Free
Application fields: Mathematics.
Description: Collection of mathematical software, papers, and
References: Netlib

Neutron Scattering Software

Entered: Wed Dec 4 16:47:10 NFT 1996
Operating systems: .
Distribution: Free
Application fields: Scattering, Materials Science.
Description: Neutron Scattering Software
References: Neutron Scattering Software List

Nuages

Entered: Wed Dec 4 16:47:47 NFT 1996
Operating systems: .
Distribution: Free
Application fields: Biology, Minerals, Structure determination.
Description: Reconstructing the 3D surface of an object of which only
References: ftp://ftp-sop.inria.fr/prisme/NUAGES/Nuages/

Nucleic acid

Entered: Wed Dec 4 16:47:47 NFT 1996
Operating systems: .
Type: Source.
Distribution: Free
Application fields: Biology.
Description: Nucleic acid sequence interpretation
References: /sincris-top/logiciel/prg-nucacid.html

O [top]

Entered: Wed Dec 4 16:47:47 NFT 1996
Operating systems: .
Application fields: Biology.
Description: Protein crystal package
References: WWW O , ftp://rose.bmc.uu.se

OASIS

Entered: Tue May 30 8:10:36 DFT 2000
Operating systems: Unix, MacOS, Windows, VMS, .
Type: Source.
Languages: Fortran.
Distribution: Free
Application fields: Biology, Structure determination.
Bibliography: J. Appl. Cryst. (2000)33,2,980-981
Description: Allows to break the phase ambiguity in One-wavelength Anomalous Scattering or Single Isomorphous Replacement (Substitution) protein data. The phase problem is reduced to a sign problem once the anomalous-scatterer or the replacing-heavy-atom sites are located. Applies a direct method procedure to break the phase ambiguity intrinsic to OAS or SIR data.
References: http://www.dl.ac.uk/CCP/CCP4/dist/html/oasis.html

ORTEP

Entered: Tue Feb 8 10:00:30 NFT 2000
Operating systems: MacOS, Windows, Linux.
Languages: Fortran.
Distribution: Free
Application fields: Graphics, visualization, virtual reality, Structure determination.
Description: ORTEP III, the Oak Ridge Thermal Ellipsoid Plot for drawing crystal structure illustrations. Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites.
References: http://www.ornl.gov/ortep/ortep.html , http://tutor.oc.chemie.tu-darmstadt.de/~martin/ortep.html

ORTEX

Entered: Mon Sep 6 9:48:32 DFT 1999
Operating systems: Windows.
Distribution: Free academic
Application fields: Structure determination.
Description: Study and display of crystal structures, thermal ellipsoid plots, mouse based interactive editing of Shelx files with auto atom sort. RASTEP and 0RENDER have 0been added to the system giving realistic rendered 3D pictures from the same view as ORTEX direct from Shelx.INS files.
References: http://www.nuigalway.ie/cryst/ , http://ccp14.sims.nrc.ca/ccp/web-mirrors/ortex/cryst/index.html , ftp://ftp.minerals.csiro.au/pub/xtallography/ccp14/ccp/web-mirrors/ortex/cryst/index.html

ORTHON

Entered: Wed May 24 10:30:43 DFT 2000
Operating systems: Unix, Windows, VMS.
Type: Source.
Languages: Fortran.
Distribution: Free
Application fields: Structure.
Bibliography: J. Appl. Cryst.. (2000). 33, 995-996
Description: Transforms any non-orthonormal cell data and atomic coordinates to orthonormal data.
References: http://cuvic.chungnam.ac.kr/~ihsuh/

ObjCryst++

Entered: Mon Jan 21 16:46:24 NFT 2002
Operating systems: MacOS, Windows, Linux.
Languages: C++.
Distribution: Free academic
Application fields: Mathematics, Topology, symmetry, Teaching.
Description: Object oriented Crystallographic Library
References: http://objcryst.sourceforge.net/ObjCryst/

Olex

Entered: Wed Jan 13 16:46:55 NFT 2004
Operating systems: Windows.
Distribution: Free
Application fields: Topology, Structures.
Description: Visualisation and topological analysis of the extended structures. The user can also measure bond lengths, interatomic distances, angles between bonds and planes; create centroids and more.
References: http://www.ccp14.ac.uk/ccp/web-mirrors/lcells/olex_index.htm

Optical constants software

Entered: Wed Dec 4 16:46:55 NFT 1996
Operating systems: Windows.
Distribution: Free
Application fields: Materials Science.
Description: optical constants software
References: /sincris-top/logiciel/prg-moxgraph.html

OrientExpress

Entered: Fri Sep 10 12:25:39 DFT 1999
Operating systems: Windows.
Type: Binary.
Distribution: Free
Application fields: Graphics, visualization, virtual reality, Materials Science, Topology, symmetry.
Description: To orient a single crystal of known unit cell dimensions from a single Laue pattern. This pattern can be registered on a flat or cylindrical detector : X Rays film, two-dimentional sensitive detector, bitmap picture. The program was succesfully applied to X rays (normal wavelength and hard X rays) and neutrons experiments, as well as to every sort mineral, organic and protein) of crystals.
References: http://www.ccp14.ac.uk/ccp/web-mirrors/lmgp-laugier-bochu/

Ortep-3 for Windows

Entered: Mon Mar 17 8:23:30 NFT 1997
Operating systems: Windows.
Type: Binary.
Distribution: Free academic
Application fields: Graphics, visualization, virtual reality.
Bibliography: L. J. Farrugia, J. Appl. Cryst. 1997 (in press)
Description: Ortep-3 for Windows is a GUI based version of ORTEP-III, with several extra facilities including mouse labelling and facilities for directly reading SHELX, CIF, CSD-FDAT, CRYSTALS, GX, SPF format atomic coordinate file.
References: http://www.chem.gla.ac.uk/~louis/ortep3/

Oscail

Entered: Wed May 13 9:48:23 DFT 1998
Operating systems: Windows.
Type: Binary.
Languages: Fortran.
Distribution: Free academic
Application fields: Structure determination.
Description: Oscail acts like a shell program setting the Jobname and Current directory and running any of ABSEN, GENINS,SHELXS-86, SHELXS-97, SHELXL-97-2, ORTEX6f. RASTEP and RENDER have now been added to the system and rendered pictures are produced from the same view position as in ORTEX. Oscail returns when any of the programs terminate. Oscail requires WIN95 or NT 4.0 and version 6f of software from Galway crystallography.
References: http://www.ucg.ie/cryst/oscail.htm

Oucy

Entered: Tue Sep 11 12:58:48 DFT 2001
Operating systems: Windows.
Type: Binary.
Distribution: Commercial
Application fields: Graphics, visualization, virtual reality.
Description: Visualisation of crystalline structures with a simple and easy to use navigation system. Features all of the most important cystalline structures such as Body-Centered Cubic, Face-Centered Cubic and others..
References: http://www.gel.ulaval.ca/~dumais01/oucy/

Ovione

Entered: Tue Mar 13 17:01:18 NFT 2001
Operating systems: Irix, Cray, Linux, VMS.
Type: Source.
Languages: Fortran.
Distribution: Free academic
Application fields: Biology, Structure determination.
Bibliography: J. Appl. Cryst. (2000)33,6, 1436
Description: Vector-search rotation-function program intended for macromolecular crystal-structure determination by the molecular-replacement method.
References: http://www11.uniovi.es/~mr/ovione/ovione_main.html

Oxford Protein

Entered: Wed Dec 4 16:47:52 NFT 1996
Operating systems: Unix, Windows, VMS.
Application fields: Biology.
Description: Programmes - Information
References: /sincris-top/logiciel/prg-oxprot.html

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