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NetSci: Structural Chemistry Software Listing             Welcome to NetSci'sList of Crystallography SoftwareNotice:Statements and opinions made for theproducts within this listing were supplied by their owners. NetworkScience Corporation assumes no responsibility for the content ofthese listings. All product and company names mentioned in thispublication are patents, trademarks, registered trademarks orservicemarks of their respective holders. The Tabular SoftwareListings portion of this site are Copyright © 1995/2006 byNetwork Science Corporated. All rights reserved.The Software Section of NetSci is accessed by hundreds of scientists every week. Our goal is to make this resource as comprehensive as possible. Ifyour software program is not included, please send e-mailwith a brief description, the categories under which your programshould appear, the platforms supported, and contactinformation.For programs currently listed in NetSci, please check the table anddescription andnotify usof any changes or additions.[A, B, C ] -- [D, E, F ] -- [G, H, I ] -- [J, K, L ][M, N, O ] -- [P, Q, R ] --[S, T, U ] --[V, W ] -- [X, Y, Z]--- A, B, C --- ABSEN A PC-based program for listing systematic absences and space-group determination. ABSORB- Brennan-Cowan X-ray absorption, reflection and dispersioncalculation. Calculates f' and f'' based on theoretical work ofCromer and Liberman calculates Rayleigh and Compton cross-sectionbased on McMaster. Absorbtion package SSRL Fortran package for calculating absorption for X-Rays Alscript program for formatting multiple sequences alignments Amas Automatic analysis of multiple protein sequence alignments. Amps Multipleprotein sequence alignment and flexible pattern matchingprograms. ARITVE is a program for modeling amorphous meantridimensional structure by a Rietveld-type approach (refiningatomic coordinates against neutron or/and X-ray interferencefunctions). It is a freeware. FORTRAN sources are available forDEC-ALPHA-AXP running VMS. Located at URL :ftp://aviion.univ-lemans.fr/pub/fluorlab/aritve.html.There also is available an example data set of a compendium ofworks related to ab initio structure determination frompowder diffraction data. Assp SGI programfor multiple sequence alignment. Estimates the lower limit inaccuracy one should expect for a perfect consensus secondarystructure prediction. AXESProgram for X-ray powder diffraction data evaluation that isspecially designed for peak-shape analysis and data preparation forRietveld refinement in connection with the FULLPROF program. Benchmark forCrystallography by the San Diego Supercomputing center. BREADTH APC-based program for powder line broadening analysis C2*X-GEN processes X-ray diffraction data formacromolecular X-ray crystallography. You can take input frommultiple detectors and rapidly index and clean up the data - makingit suitable for input to refinement packages such as X-PLOR. CamelJockey - absorption correction programs Ca.R.Ine is a crystallography program for Mac andWindows. Includes 2D and 3D visualization, stereographic projectionand more. CaRIne is available fromDIVERGENT S.A.CaRIne Crystallography Software17 rue du Moulin du RoyF-60300 SenlisFrancePhone/Fax : +33 3 44 53 44 67e-mail : cyrille.boudias@wanadoo.frhttp://pro.wanadoo.fr/carine.crystallography CCP4 (Collaborative Computational Project). An integratedsuite of nearly 100 programs for protein crystallography.Application areas include data processing, scaling, Pattersonsearch and refinement, molecular replacement, structure refinement,phasing and more. The programs can be obtained via anonymous FTPfrom gserv1.dl.ac.uk:pub/ccp4. Contact:David LoveDaresburry Laboratory (SERC)Keckwick LaneWarrington WA4 4ADGreat BritainTel: +44 925 603530Fax: +44 925 603100E-mail: info-server@daresbury.ac.uk CCP14 (CollaborativeComputational Project). An integrated suite of programs for proteincrystallography. CHAIN is a computer graphics program designed to fitatomic coordinates to electron density maps. Features includeability to use multiple coordinate files, regulation ofcoordinates, a selection of display modes, plotting capabilitiesand a scripting language. Contact: Andrew Shraff, Howard HughesMedical Institute, One Baylor Plaza, Houston, TX 77030 USA; Tel:713-798-6563, Fax: 713-797-6718 CrystalDesigner is a tool for building, studying andvisualizing all kinds of crystal structures. It is easy to use andis ideal for both teaching and scientific studies. A crystalstructure may be viewed as a unit cell or multiples of it; as aplane with a user defined thickness or by coordination around aselected atom within a user defined ratio. Additional informationcan be found on theCrystalDesigner homepage. CrystalDiffract is user-friendly, elegant program for understanding and visualizing x-ray and neutron powder diffraction patterns from crystals. Crystallographica is a new software toolkitwhich provides the complete environment for crystallography.Microsoft Windows interface, Pascal interpreter (specially extendedwith hundreds of building block crystallograpic routines).Available from:Oxford Cryosystems3 Blenheim Office ParkLong HanboroughOxon OX8 8LN, UKTel +44 (0)1993 883488Fax +44 (0)1993 883988web site (free demo version) athttp://www.demon.co.uk/oxcryo. CrystalMaker is an award-winning PC/Mac program for building, displaying and manipulating all kinds of crystal and molecular structures - with real-time photo-realistic graphics and "out-of-the-screen" 3D display. CSDCrystal Structure Determination package (CSD) is a MS-DOS andWindows-based program for crystal structure treatment usingX-ray/neutron experimental data from either powder or singlecrystal. Crystal Studio is a comprehensive Windows 95/98/NTsoftware package for crystallography. It creates interactivephoto-realistic 3D crystal structures and their plane atomicarragement views in stunning colors and 3D realism. It also plotsinteractive powder XRD patterns, zone axis electron diffractionpatterns and stereographic projections. Powered with acrystallographic database, it lets you create stunning 3D crystalstructures and their diffraction patterns in just a few mouseclicks. Free demonstration version are available for download.Crystal Studio is a Windows 95/98/NT software forcrystallography developed by CrystalSoft Corp., our home page isat;http://www.crystalsoftcorp.com/Features list, gallery of images created and free demonstrationversion are available from the web site. Contact details are asfollows:CrystalSoft Corp.PO Box W11, WestfieldParramatta, NSW 2150AustraliaTel: +61 2 9793 2321Fax: +61 2 9793 2324e-mail: info@crystalsoftcorp.com CSECMVMRL/browser tool which can be used to study the symmetry aspectsof space groups.--- D, E, F --- Datasqueeze is a graphical interface for analyzing data from 2D x-ray detectors (image plate, CCD, wire). The data are represented as a false color image. The program provides 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, saving the image in multiple graphics formats, saving the x-y data as an ascii file, and adding or subtracting multiple data files. The x-y data extracted from the 2D images can be least-squares fits to a variety of functions.Datasqueeze runs on multiple platforms, including Windows, Linux, and Macintosh OS X. Datasqueeze is particularly 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. Datasqueeze is not well suited for extracting intensities from many sharp Bragg peaks in a single-crystal diffraction type experiment (although it has been used to extract information about pixel statistics in such images).Datasqueeze is available as a free download for a trial period of 10 days; after that it costs $100US with a 50% discount for academic users. DIFRACSingle-Crystal Diffractometer Output-Conversion DISCUS - Diffuse Scattering and Defect-structuresimulation. DRAWCRYS is a set of programs which are based onmodifications of the old Oak Ridge crystallographic program ORFEE.Included is the ORFEE source code and the complete instructionmanual. There is also a complete OFREE input file based oncytidylic acid. This is called CYTIDYL.ORF. To make sure ORFEE isworking, a test output file called CYTIDYL.OUT is also included.There is a brief description of the program in a README file.The programs are found atftp://ccl/osc.edu/pub/chemistry/software/SOURCES/FORTRAN/drawcrysIn this directory there are seven files. The FORTRAN code forthe program is called DRAWCRYS.FOR. A complied version of thisprogram is DRAWCRYS. This was complied by MS FORTRANPowerstation. DRXWinWindows-based graphical and Analytical Tools for XRD PowderPatterns. Works with files from several diffractometers. DRXWin isprovided by Dr. Vicent Primo Martin at the Max-Planck-Institut furFestkorperforschung, Heisenbergstrasse, 1 D-70569, Stuttgart,Germany. An FTP mirror at the CCP14 site is also available athttp://www.dl.ac.uk/CCP/CCP14/ccp/web-mirrors/drxwin/drxwin/ DS 4-circle Diffractometer Simulationftp://indy.polymer.hokudai.ac.jp/pub Equiv allows for the analysis and management of data collections from X-ray single crystal diffractometry (namely, a generally large set of hkl indices, together with the corresponding diffraction intensities, or structure factor, and standard deviations). It is particularly useful for high symmetry systems, where a checking of the intensities of the equivalent reflections is a good and fast way of estimating the quality of the data collected. Since the publication of the release 1.0 of the program (Prencipe M. (1998). J. Appl. Cryst., 31, 109), a number of upgrades have been done and a new graphical interface has been developed. Both Linux/Unix and Windows versions can be freely downloaded at the sitehttp://www.prencipe.net/nuova_cartella/equiv.html. Full documentation and installation instructions are provided with the package.Mauro Prencipe Dept. of Mineralogical and Petrological Sciences Univ. of Torino Via Valperga Caluso 35 10125 Torino - Italy e-mail: mauro.prencipe@unito.it ETHCrystallography - software distribution center FlexCryst is a program package for Crystal Structure Prediction, Crystal Structure Determination, and Estimation of Sublimation energy. FRODO is a molecular graphics program for crystallographyapplications. It has been replaced by a newer version of the program,TURBO FRODO. For more information, contact: AFMB - CNRS31 Chemin Joseph Aiguier13402, Marseille Cx 20France Fax : (+33) 4.91.16.45.36 FRODO/Tom is a freeware (foracademics only) version of Frodo.--- G, H, I ------ J, K, L --- Latticepatch is an interactive graphics program used bycrystallographers to evaluate data collection strategies for areadetector X-ray diffraction studies. Using Latticepatch, acrystallographer can visualize how rotation of the crystal willspread reflected X-radiation across the surface of an areadetector. Using the crystal's symmetry characteristics, itsorientation in the lab frame and the crystal-to-detector distance,Latticepatch helps the crystallographer to collect the unique datamost efficiently. The program runs on Silicon Graphics 4D seriesworkstations. Contact:Alexandra KlingerDepartment of BiochemistryHealth Sciences CenterBox 440Charlottesvile, VA 22920 USATel: 804-924-1943Fax: 804-924-5069E-mail: alk2p@virginia.edu LeoCrystal is an application for performing modeling of reaction on the surface of crystal for educational and research purposes. With it help one can estimate influence of different parameters of the structure elements of crystals on topology and kinetic of the crystallization. Because process of crystal growth is present in practically all major technology processes, in depth understanding of all its complexities is essential necessity for all material scientists.Download: http://www.leokrut.com/LeoCrystal.zipDetail description: http://www.leokrut.com/LeoCrystal.htmlPlatform - all windows OC beginning Win95.Contact informationDr. Leonid Sakharov34 Hamilton Rd., #310Arlington, MA 02474(781) 646-4048http://www.leokrut.comLeonidSakh@aol.comLsakharov@leokrut.com--- M, N, O --- MULTAN88 is ananalysis and visualization program available from MolecularStructure Corporation. O is a moleculargraphics program for protein crystallographers. The program isavailable from:T. Alwyn JonesBlueberry HillDalby, S-75591UppsalaSwedenTel: +46-18-174982Fax: +46-18-536971E-mail: alwyn@xray.bmc.uu.se ORTEPORTEP III, the Oak Ridge Thermal Ellipsoid Plot Program for CrystalStructure Illustration --- P, Q, R --- PCPDFWIN is Windows® based retrieval/display softwarefor accessing records from the ICDD Powder Diffraction Database,known as the PDF-2. Release 1998 now includes 115,000 compounds, ofwhich 20,000 are organic and 95,000 inorganic; locating anindividual pattern by scrolling through a database of this sizewould be very difficult. PCPDFWIN provides a high degree offlexibility and control in the design of search schemes so thatonly the most relevant entries need to be examined by the user.Complex searches of the PDF-2 may be carried out by combiningBoolean operators and chemical and physical properties, elementaland crystallographic information, compound names, subfiles,literature references, and/or strong lines.A FREE version of PCPDFWIN (which allows full functionality ofthe search/retrieval software within Set 31 of PDF-2 only) isavailable from the ICDD ftp site - ftp://www.icdd.com/PDF31/ - aself extracting executable. The program is made available byICDD - International Centre for Diffraction Data12 Campus BoulevardNewtown Square, PA, 19073ph : (610)325-9814fax: (610)325-9823e-mail: info@icdd.comURL: http://www.icdd.com PCSIWIN is a Windows® based computer programdesigned to provide the functionality of the Hanawalt and FinkSearch Manuals for accessing records from the ICDD PowderDiffraction Database. Data input accomodates d/I pairs for up to 40lines. If the wavelength is specified 2theta/I pairs can be used.The user can customize the size of the database by using filtersfor subfiles, chemistry, and number of elements. An automatichistory function keeps track of results from previous sessions. Thesoftware is available from:ICDD - International Centre for Diffraction Data12 Campus BoulevardNewtown Square, PA, 19073ph : (610)325-9814fax: (610)325-9823e-mail: info@icdd.comURL: http://www.icdd.com PowderCell,a development based on the DOS program POWDER CELL, runs underWindows. The aim of this program is the intuitive generation ofinitial structure models to use them in refinement procedures, e.g.in so called Rietveld programs.Contact:Dr. Gert NolzeFederal Institute for Material Research and Testing Lab. V.13Unter den Eichen 8712205 BerlinTel: +49 30 81043109Fax: +49 30 81043187 QUEST adata analysis and retrieval system for the Cambridge StructuralDatabase of small molecule organics and organometallics. It allowsthe user to design and specify a query which is then used tointerrogate the database. The database is searched sequentiallyuntil the program locates a CSD entry which matches the searchcriteria. Contact:Frank AllenCambridge Crystallographic Data CentreUniversity Chemical LaboratoryLensfield RoadCambridge CB1 2EW, U.K.Tel: +44-223-336408Fax: +44-223-336033E-mail: software@crystallography.chemistry.cambridge.ac.uk QuickPDBSequence/Structure Search and Display. Programs are used to find astructure in the Brookhaven PDB based upon a text or sequencesearch and then to render that structure with the ability to markup fragments in the sequence and see them accordingly in structureview. Renex is diffraction patterns editor and analyzer with"WYSIWYG" approach. It has been designed to works with overlappedpeaks and "non-ideal" or "noisy" patterns. Renex works with anyangle-dispersive X-Ray and Neutron Powder diffraction patternsfiles. It is a shareware. Platforms include Windows 95/98/NT.Additional information on Renex is available from:http://www.chat.ru/~meola--- S, T, U ---SingleCrystal is software for simulating diffraction patterns from single crystals, visualization of diffraction space and displaying stereographic projections of lattice planes. SnB(Shake-and-Bake) implements the Shake-and-Bake method ofcrystal structure determination. This is a direct methods phasingalgorithm which alternates refinement in reciprocal space withdensity modification in real space to reduce the value of theMinimal Function. Contact:Russ Miller or Charles M. WeeksDept.of Molecular BiophysicsHauptman-Woodward Medical Research Inst. 73 High StreetBuffalo, NY 14203Tel: 716-856-9600Fax: 716-852-6086E-mail:snb-request@hwi.buffalo.edu. SIR92 is a program for theautomatic solution of crystal structures by directmethods. SIRPOW.92 is a program for theautomatic solution of crystal structures by direct methodsoptimized for powder data. teXsan crystallographic software package contains acomprehensive set of algorithms for the analysis of small moleculesingle crystal X-ray data. The suite of programs is unified under auser-friendly graphical user interface (GUI). Modules include:bioteX, an area detector processing software. The newbioteX program suite facilitates the collection, processing andinterpretation of data from the Rigaku R-AXIS Imaging Plate AreaDetector and MSC CCD detector. The suite of programs is unifiedunder a user-friendly OSF/Motif based graphical user interface(GUI).SQUASH, a tool for phase refinement and extension onlarge structures. The starting point is a set of native structurefactors to some resolution, and estimated phases and figures ofmerit for some subset of the phases. The result is a set ofimproved phases and figures of merit for the whole data set.TeXsan is available from:Molecular Structure Corporation3200 Research Forest DriveThe Woodlands, TX 77381Tel: (713) 363-1033FAX: (713) 364-3628 TOPOS 3.2 is a program package for multipurpose geometrical and topological analysis of crystal structures. It provides the working with crystal structure databases and the calculation of the geometrical and topological characteristics of crystal structures in these databases. TOPOS 3.2 is an integrated interactive shell including database management system (DBMS), which allows one to edit, search and retrieve crystal structure information, and a number of applied programs integrated into DBMS. The version 3.2 includes seven applied programs.The homepage of the TOPOS program package for multipurpose geometrical and topological analysis of crystal structures is supported by:Prof. Vladislav A. BlatovSamara State UniversityAc. Pavlov St. 1Samara 443011RussiaPhone: 7(8462)345445FAX: 7(8462)345417Email: blatov@ssu.samara.ru--- V, W ------ X, Y, Z --- X-AUTOFIT provides interactive automated tools for denovo carbon alpha tracing into electron density maps. AvailablefromAccelrys as a part of the QUANTA environment. X-BUILD is designed for model building molecularcoordinates into electron density and is closely linked withX-AUTOFIT. Interactive automated tools help you to significantlyspeed up the process of fitting your electron density map.Available fromAccelrys as a part of the QUANTA environment. X-PLOR integrates nuclear magnetic resonance data andand X-ray crystallographic diffraction data with molecularmechanics, dynamics, and energy minimization to aid in the solutionof three-dimensional molecular structures. You can accelerate thestructure determination process for biological macromoleculesincluding proteins, nucleic acids, and protein-ligand complexes.Available fromAccelrys as a part of the QUANTA environment.X-PLOR/Refine is an X-ray structure determination programthat integrates crystallographic diffraction data with molecularmechanics, dynamics, and energy minimization to aid in the solutionof three-dimensional structures. Available from Accelrys as a part of the Insight II environment. Xsight integrates all of the major computational techniques for macromolecular crystallography. You can analyze andinterpret X-ray data, build models of protein structures and relatethem to electron density, refine structure against X-ray data,analyze structures for symmetry, and visualize and validatestructure. Available fromAccelrys as a part of the Insight II environment. X-SOLVATE automatically places water molecules intoelectron density maps. Available fromAccelrys as a part of the QUANTA environment.X-PLOR GUI Graphic User Interface is used to edit, submit andmonitor X-PLOR jobs via Web forms. Xtalis a package for structure resolution. Reequires the use of theRatmac Fortran preprocessor Xtaldraw is Windows-based interactive computer graphics program that displays and manipulates ball and stick, polyhedral and thermal ellipsoid colored drawings of any crystal structure or molecule, and render a diffraction pattern for X-ray, energy dispersive, or neutron radiation. It also has the capacity to compute geometrical parameters and a TLS modelling of the rigid-body thermal motion of polyhedral groups. It can be configured to link seamlessly to the American Mineralogist Crystal Structure Database, a website containing thousands of crystal structures of major interest to the mineralogical community. The database is located at: http://rruff.geo.arizona.edu/AMS/amcsd.php XtalView - a macromolecular display and rendering package |
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