Infobox software name RasMol logo screenshot Image Rasmol1.png 275px caption Example of rendering by RasMol. TRAF2 trimer PDB 1DOA collapsible author Roger A. Sayle developer Herbert J. Bernstein released latest release version 2.7.5.1 latest release date release date 2009 07 17 latest preview version latest preview date frequently updated programming language C programming language C operating system platform size language status genre Molecular graphics license GNU General Public License website http www.rasmol.org RasMol is a computer program written for molecular graphics visualization intended and used primarily for the depiction and exploration of Structural biology biological macromolecule ... Sayle in the early 90s ref Roger Sayle and E. James Milner White. RasMol Biomolecular graphics for all ... the software to run on then modestly powerful personal computer s. Before RasMol, visualization software ran on graphics workstations that, due to their expense, were less accessible to scholars. RasMol ... in structural biology. RasMol has a complex version history. Starting with the series of 2.7 versions ref Herbert J. Bernstein, Recent changes to RasMol, recombining the variants, Trends in Biochemical Sciences TIBS , September 2000, Vol. 25, No. 9, pp. 453 455 ref , RasMol is licensed under a dual ... plus sons.com software RasMol 2.7.3 doc RASLIC RASLIC license ref . RasMol includes a computer ... software Sirius has incorporated the RasMol scripting language into its commands. Protein ... electron microscopy electron microscopy . Inter process Communication On UNIX platforms Rasmol ... rasmol Download RasMol production releases http blondie.dowling.edu projects rasmol Development ... microbio rasmol pershist.txt Early RasMol development history http www.rasmol.org history.html Later RasMol development history Interlang Categories Category Bioinformatics software Category ... ca RasMol de RasMol fr Rasmol it RasMol ml pl RasMol ru RasMol ... more details
and data structures developed as a part of http mbt.sdsc.edu Molecular Biology Toolkit . RasMol compatible scripting Commented out because image was deleted Image Sirius rasmol import.png right thumb 275px Image of a molecular scene encoded by a RasMol script. Created using Sirius. Sirius features .... The set of commands has been patterned after RasMol , so it s fully compatible with existing scripts ... structures loaded at the same time, and to enable more flexible selection. Existing RasMol ... scenes. Since RasMol uses a coordinate system that differs from that Sirius, internal conversion is performed when RasMol scripts are imported, so that any orientation changes are shown correctly ... more details
Multiple issues context July 2009 refimprove July 2009 This list of software for protein structure visualization is a compilation of bioinformatics software used to view protein structure s. Such tools are commonly used in molecular biology , and bioinformatics . border 0 align center style border 1px solid 999 background color FFFFFF align left bgcolor CCCCCC NAME Link Author BioBlender http www.bioblender.eu BioBlender official web site SciVis team Visual Molecular Dynamics http www.ks.uiuc.edu Research vmd VMD official website Jmol http www.jmol.org Jmol official web site Jmol development team Geneious Geneious Pro implemented Jmol viewer as part of an all in one sequence analysis software package http www.geneious.com Geneious homepage Geneious development team PyMOL http www.pymolwiki.org index.php Main Page PyMOL Wiki Warren Lyford DeLano RasMol http www.rasmol.org Official website Roger Sayle UCSF Chimera http www.rbvi.ucsf.edu chimera Official website UCSF RBVI STING http www.cbi.cnptia.embrapa.br SMS STAR STING Friend http ilyinlab.org friend Valentin Ilyin http www.molsystems.com vp3ds.html VisProt3DS 3D Stereoscopic view anaglyth, side by side, hardware http www.molsystems.com vp3ds.html Official website Nick Vtyurin http polyview.cchmc.org polyview3d.html Polyview 3D Web based high resolution static views and animations using Pymol or Rasmol http polyview.cchmc.org polyview3d.html Official website Aleksey Porollo & Jarek Meller See also Biological data visualization List of molecular graphics systems List of Open Source Bioinformatics software List of software for molecular mechanics modeling List of nucleic acid simulation software Molecular graphics Category Bioinformatics Category Lists of software Protein Structure Category Bioinformatics software science software stub ... more details
Infobox Software name MDL Chime logo screenshot caption collapsible author Elsevier developer Symyx Technologies released Start date 1998 latest release version 2.6 SP7 latest release date Start date and age 2007 07 31 latest preview version latest preview date Start date and age YYYY MM DD frequently updated programming language operating system Mac OS , Microsoft Windows platform Internet Explorer , Mozilla Firefox size language status genre license website http accelrys.com products informatics cheminformatics chime no fee.php Accelrys Chime MDL Chime is a free Plug in computing plugin used by web browsers to display the 3D computer graphics three dimensional structures of molecules . It is part of the ISIS product line acquired by Symyx Technologies from scientific publisher Elsevier in October 2007. It is based on the RasMol code. Chime is used by a wide range of biochemistry web sites for the visualization of macromolecules . Many of these sites are linked to the World Index of Molecular Visualization Resources http molvisindex.org MolVisIndex.Org . Chime was also used until 2006 at the Protein data bank Protein Data Bank to examine structures stored there. Although available in 1998 in both Windows 98 and Mac OS 9 versions for both Netscape and Internet Explorer browsers, development of Chime did not follow the move to Mac OS X for the Mac and support for Windows based browsers other than Internet Explorer was dropped although it works well in Mozilla Firefox . No significant features have been added since 1998 except for updates in the installation package to follow the development of Windows and Internet Explorer. Chime largely has been superseded by Jmol . Jmol is a non proprietary open source Java molecular visualization application applet that has maintained most Chime command compatibility while adding features. A feature of Chime which is not yet reproduced with Jmol is the calculation of electrostatic or hydrophobic potential for use in coloring molec ... more details
Image VitaminB12 2.png thumb 300px right An example of a diagram drawn using ISIS Draw ISIS Draw was a chemical structure drawing program for Windows, published by MDL Information Systems . It was available free of charge for academic and personal use. It acted as a front end to ISIS Base, a chemical database program from the same company, as well as some other ISIS Integrated Scientific Information System products. The first version of the program was released in 1990, and the last version was 2.5 in 2002 it has since been superseded by Symyx Technologies Symyx Draw . ISIS Draw used its own proprietary file format, with the extension .skc, and also supported standard chemical file format s such as MDL molfile , Rxnfile, and TGfile. Because of its role as a database query preparation program, ISIS Draw supported a variety of special atom and bond types used for substructure search ing, such as wildcard atoms, aromatic bonds, and ring bonds, as well as atom mapping, required for reaction searches. While ISIS Draw was mainly a 2D drawing program, it had some 3D rotation features and could interface with Rasmol for 3D visualization and rendering. ISIS Draw also included structure and reaction validation features and could calculate elementary properties such as formula and molecular weight. Now Accelrys Draw is served as a replacement of ISIS Draw. The newest version is 4.0, as of March 2011. As ISIS Draw, the program is available free to academics. References cite journal title Personal Experience with Four Kinds of Chemical Structure Drawing Software Review on ChemDraw, ChemWindow, ISIS Draw, and ChemSketch author Li, Z. Wan, H. Shi, Y. Ouyang, P. journal J. Chem. Inf. Comput. Sci. year 2004 volume 44 issue 5 pages 1886 1890 doi 10.1021 ci049794h pmid 15446849 cite book title Chemoinformatics A Textbook author Johann Gasteiger, Thomas Engel publisher Wiley VCH year 2003 isbn 3527306811 page 143 Dalby, A. Nourse, J. G. Hounshell, W. D. Gushurst, A. K. I. Grier, D. L. ... more details
Infobox Software name Extensible Computational Chemistry Environment ECCE developer Pacific Northwest National Laboratory latest release version 6.3 latest release date release date 2012 04 4 operating system Linux , Microsoft Windows with a XServer program that supports OpenGL , Mac OS X license EMSL Software User Agreement website URL 1 http ecce.pnl.gov 2 ecce.pnl.gov Extensible Computational Chemistry Environment ECCE The Extensible Computational Chemistry Environment ECCE, pronounced etch provides a sophisticated graphical user interface , scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies. Major features Support for building Molecular modelling molecular models . Graphical user interface to a broad range of electronic structure theory types. Supported codes currently include NWChem , GAMESS UK , Gaussian 03, Gaussian 98, and Amica. Other codes are registered based on user requirements. Graphical user interface for basis set chemistry basis set selection. Remote submission of calculations to UNIX and Linux workstations , Linux Cluster computing clusters , and supercomputers . Supported queue management systems include PBS, LSF, NQE NQS, LoadLeveler and Maui Scheduler. Three dimensional visualization and graphical display of molecular data properties while jobs are running and after completion. Molecular orbital Molecular orbitals and Vibrational frequency vibrational frequencies are among the properties displayed. Support for importing results from NWChem, Gaussian 94, Gaussian 98, and Gaussian 03 calculations run outside of the ECCE environment. Extensive web based help. See also columns list 2 NWChem Molden Avogadro software Gabedit Molekel PyMol Visual Molecular Dynamics VMD Jmol RasMol Ascalaph Designer External links Official http ecce.pnl.gov name ECCE homepage U ... more details
with an already downloaded version of molecular structure viewer e.g. Cn3D , Rasmol .... Once the BLAST ... for viewing structure of molecules from Protein Data Bank PDB e.g. Cn3D, Rasmol, SwissPDB etc. Further ... more details
molecular surfaces coloured by electrostatic or hydrophobic potential. Originally based on RasMol ... 2009 ref Provided by DNASTAR RasMol free and open source C programming language C stand alone ... RASMOL biomolecular graphics for all volume 20 issue 9 pages 374 journal Trends in Biochemical Sciences ... Bernstein first1 HJ title Recent changes to RasMol, recombining the variants volume 25 issue 9 pages ... http www.rasmol.org title Home Page for RasMol and OpenRasMol accessdate 24 September 2009 Self published ... more details
products qmol index.html DNASTAR, Inc. RasMol Y Fast viewer Free http www.bernstein plus sons.com software rasmolRasMol Raster3D Y High quality raster images Free http skuld.bmsc.washington.edu ... more details
educational software like Dr. Geo , Rasmol , K Tech lab , Geogebra , Chemtool , Kalcium etc. are being ... office , GIMP , Dr. Geo , Rasmol , KEduca , Klab etc. Examination software to conduct IT practical ... more details
Column R is the scheme used by Rasmol when two colors are shown, the second one is valid for versions 2.7.3 and later. ref name jmol ref name rasmol http www.bio.cmu.edu Courses BiochemMols RasFrames CPKCLRS.HTM Rasmol color table at bio.cmu.edu. Accessed on 2010 01 28. ref All colors are approximate ... more details
his RasMol program into the public domain. RasMol contained a very high performance molecular renderer ... 1992, 1993 RasMol , Kinemage Platform independent MG. Molecular Design Limited MDL van Vliet, Maffett ... Altman and historical slides. http www.umass.edu microbio rasmol history.htm History of Visualization ... more details
software sampler s div id ALC ALC div Molecular coordinates Alchemy , RasMol div id ALG ALG ... Chapter information Ventura Publisher div id CIF CIF div Crystallographic Information File RasMol ... coordinates CHARMM , RasMol div id CRDOWNLOAD CRDOWNLOAD div Google Chrome download in progress Google ... more details
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