121. RasMol Home Page mouse. molecular Visualization Freeware Protein Explorer, Chime RasMol RasMol). New to molecular Visualization? Check out Gallery http://www.umass.edu/microbio/rasmol/

Oxy-hemoglobin zooming in to oxy-heme (from 1hho.pdb by B. Shaanan ). This is an animated picture ; unlike with Protein Explorer , you cannot move it with your mouse. Molecular Visualization Freeware Protein Explorer Chime RasMol This is the RasMol Home Page visited by over 500,000 people from over 115 countries! Contents What's New? ... Protein Explorer a RasMol-derivative, is the easiest-to-use and most powerful software for looking at macromolecular structure and its relation to function. And it's free! It runs on Windows or Macintosh/PPC computers. ( linux users see below .) RasMol users will find its menus very familiar, and it understands RasMol commands. It is very fast: rotating a protein or DNA molecule shows its 3D structure. If you have never seen this, watch the image at the upper right of this page. (Click here to see another molecule rotate .) Look at our gallery to see still snapshots of other molecules. Also available here are Chime-based tutorials on DNA Hemoglobin Antibody The Protein Morpher ... Infrared spectra with animated molecular vibrations Tutorials on many other popular molecules Chime , freeware from MDL, and derived from RasMol. Here are reference materials and templates about

122. CHEMICAL BONDS, MOLECULAR SHAPES, AND MOLECULAR MODELS . This hypermediabased tutorial on chemical bonds, molecular shapes......Chemical Bonds, molecular Shapes, and molecular Models. http://www.eou.edu/chemweb/molmodel/mmp1.html

Chemical Bonds, Molecular Shapes, and Molecular Models Description This hypermedia-based tutorial on chemical bonds, molecular shapes, and molecular models is designed to supplement lecture material and to prepare students for model building in the laboratory, classroom, or at home. It provides not only the material fundamental for chemical model building, but contains more basic information to reacquaint students with topics in which they need to strengthen their foundation. It also contains "hyperactive molecules", three-dimensional structures that students can rotate and manipulate similarly to molecular model kits conventionally used in the laboratory. In addition digital photos provide step-by-step instructions on how to assemble molecular structures. Instructions In this tutorial viewing and manipulation of 3D models of molecules requires that the MDL Chemscape Chime plug-in be installed in your computer. It also requires or higher version. If you are viewing this tutorial from an EASTERN computer laboratory, your computer should already be configured with the Chime plug-in. View the

123. MMTK Home Page MMTK is based on an objectoriented model of molecular systems. A system is made up of atoms, molecules, and complexes, all of which http://starship.python.net/crew/hinsen/MMTK/

Sections Documentation Examples Download Useful links See also MMTK Wiki Python ScientificPython DomainFinder Contact hinsen@llb.saclay.cea.fr The Molecular Modelling Toolkit The Molecular Modelling Toolkit (MMTK) is an Open Source program library for molecular simulation applications. In addition to providing ready-to-use implementations of standard algorithms, MMTK serves as a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular simulations. The three most common usage patterns of MMTK are Writing Python scripts that make use of MMTK functions for standard simulation and modelling applications. This is similar to using other simulation packages with a scripting language (i.e. CHARMM or Gromos), but with the added advantage of having access to lots of useful Python modules from elsewhere. The example section shows what such scripts look like. Writing modules that interact closely with MMTK (and perhaps other packages) to solve problems for which no standard solution exists. For example, adding a particular force field term or a particular simulation or analysis algorithm. There is not much competition for MMTK in that domain. Writing application programs in Python that use MMTK internally, for users that do not need to know anything about such internals. Those programs can provide easy-to-use graphical interfaces (see e.g.

124. Department Of Pharmaceutical Information Science-Tokyo University A comprehensive listing of 3D molecular structures for Japanese prescription pharmaceuticals which can be viewed with either the Chemscape Chime plugin or the http://www.ps.toyaku.ac.jp/dobashi/

125. Virtual Student Model Kit WWU Virtual molecular Model Kit. More Small Molecules in RasMol or Chime Format molecular Models at Okanagan University College. This page is maintained by Prof. http://atom.chem.wwu.edu/dept/vmolckit/molecule.html

WWU Virtual Molecular Model Kit This page was created for our organic chemistry students (Chemistry 351) who might prefer using the computer to a physical model set. However, we hope others will also enjoy using it. Below are a variety of instructional molecules that can be viewed if you have installed either RasMol or Chemscape Chime as a plug-in viewer in your web browser. At the bottom of the page are links to some other RasMol and Chime sites. These molecules can be Interactively sized and rotated. - Left mouse button = rotate. - Shift + left mouse button = zoom. - Right mouse button = translate if using RasMol. - With RasMol the menus are at the top of the window. - With Chime pressing the right mouse button brings up the menus. Most of these molecules can be viewed best by using the "Sticks" option under the Display menu. Have Fun !!! Organic Molecules Alkanes methane ethane eclipsed ethane staggered butane eclipsed (0) ... hexane - all anti Cycloalkanes C3-C5 cyclopropane cyclobutane folded cyclobutane planar cyclopentane envelope ... cyclopentane half-chair Cyclohexane Chair cyclohexane chair cyclohexane axial H coded cyclohexane equatorial H coded .....Compare axial and equatorial H's side by side

126. NAMD - Scalable Molecular Dynamics simulation code NAMD can simulate a solvated allatom model of ATP NAMD an order of magnitude ahead of comparable packages for molecular dynamics simulation. http://www.ks.uiuc.edu/Research/namd/

Overview Research Development Dissemination ... NIH Resource for Macromolecular Modeling and Bioinformatics NAMD, recipient of a 2002 Gordon Bell Award , is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects , NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our all-new tutorials show you how to use NAMD for biomolecular modeling. Spotlight: More Commodity Supercomputing (Jul 2001) Our low-cost cluster of 32 Athlon PCs (see February 2001 highlight ) has been in constant use by local users, providing a substantial and very cost-effective boost to our group's large-scale simulation capabilities. To satisfy demand, we have added two additional 32-processor clusters with higher performance at an even lower cost. On this platform, the freely available simulation code

127. Computational Molecular Biology At NIH Tools such as GCGLite+ (NIH only) Molecules R Us, and Blast. Includes GCG documentation (NIH only) and the NIH GCG FAQ Databases for molecular Biology. http://molbio.info.nih.gov/molbio/

Analysis Documentation Databases Desk Reference ... SeqWeb - a web interface to GCG (NIH only, Helix username/password required) WHALES - Web Homology Alert Service (NIH only) Sequence Analysis tools at NIH and around the world. Tools such as GCG-Lite+ (NIH only) Molecules'R'Us , and Blast Documentation and Information about sequence analysis tools and programs. Includes GCG documentation (NIH only) and the NIH GCG FAQ Databases for Molecular Biology. Includes nucleotide databases (e.g. Genbank protein databases chromosome maps enzyme databases , etc. Molecular Biology Desk Reference A collection of basic information such as the genetic code and WebElements Periodic Table , protocols and tutorials. Software repositories Sites which provide access to molecular biology and sequence analysis software. Other Molecular Biology Resources LInks to major Web sites with Molecular Biology resources. Maintained by the High Performance Scientific Computing Section Center for Information Technology National Institutes of Health

128. Molecular Model Sets: Molymod Organic Chemistry, Biochemistry, Stereochemistry, Molymod molecular model sets for organic and AP chemistry, molecular biology, stereochemistry, complex ions, VSEPR theory, orbital hybridization and symmetry. http://www.indigo.com/models/molymod-molecular-model-sets.html

Molymod Molecular Model Sets Home Search All Molecular ... Indigo.com Molymod® Molecular Model Sets M olecular model sets are configured for specific areas of study such as organic chemistry, biochemistry, stereo-chemistry, VSEPR theory, crystal lattices, etc. They include 10 or more types of components and permit building structures specific to those interest areas. Organic Chemistry Student Sets Set 62053 is our best buy and most versatile. It is intended for university level organic and inorganic chemistry and can be augmented for use in VSEPR theory and biochemistry. It can be used to show open, hybrid or semispacefilling representations of molecules. Set 62009 is designed specifically for organic and inorganic chemistry for high school college level. It supports only open style models. Both sets can be augmented with extra Molymod Components. Orders/quotes: click the shopping cart icon; change quantities if desired; choose a shipping method; choose payment method. Student Sets Click on images for more info. Use set 62053 for VSEPR theory, molecular hybridization, AP chemistry.

129. Molecular Compounds Coordinate Covalent bonds. molecular and Structural Formulas. Drawing Lewis Structures. Naming Binary Molecules Compounds. Properties of molecular Compounds. http://scidiv.bcc.ctc.edu/wv/5'/0005-000-TOC.html

Table of contents Covalent compounds Dr. Walt Volland Formative exercise Formative exercise answers Suggested exercises Covalent bonds ... Self test answers i Click here to access The Molecule of the month page at the University of Oxford. Click here to access The Molecule of the month page at the University of Bristol.

130. Accelrys - Formerly Oxford Molecular Oxford molecular is now Accelrys. Oxford molecular was incorporated into Accelrys Inc. on June 1, 2001. Cheminformatics. Oxford molecular History. http://www.oxmol.co.uk/

@import url(/styles/about2002.css); /*IE and NN6x styles*/ CORPORATE OVERVIEW NEWSROOM EVENTS EMPLOYMENT ... CONSORTIA MEMBERS About Accelrys Corporate overview News room Events Employment ... About Accelrys Oxford Molecular is now Accelrys Oxford Molecular was incorporated into Accelrys Inc. on June 1, 2001. Accelrys, the leader in simulation and informatics software for the pharmaceutical and chemicals process industries, was created from the combination of Oxford Molecular, Synopsys MSI , and GCG Accelrys homepage Accelrys launch press release Oxford Molecular was a leading provider of cheminformatics tools. For full details of our cheminformatics solutions see: Cheminformatics Oxford Molecular History Founded in 1989, Oxford Molecular was listed on the London Stock Exchange in 1994. The Oxford Molecular Group grew aggressively through internal growth and the acquisition of software and experimentation-based companies. Acquired companies included Chemical Design Limited, MLR Automation, and the Genetics Computer Group (GCG).

131. This Link Has Changed!! Look Now At This link has changed!! Look now at http//scsg9.unige.ch/fln/eng/toc.html Francois Savary, savary@sc2a.unige.ch. Group of Professor http://scsg9.unige.ch/eng/toc.html

This link has changed!! Look now at : http://scsg9.unige.ch/fln/eng/toc.html Francois Savary, savary@sc2a.unige.ch Group of Professor J. Weber, Department of Physical Chemistry,University of Geneva 30, quai Ernest Ansermet CH-1211 Geneva 4 Switzerland

132. Deep View (Swiss-PdbViewer) Tutorial http://www.usm.maine.edu/~rhodes/SPVTut/

An alternative is to download the offline version and open individual pages from the folder. Click here to obtain the offline version. Use Zipit or Stuffit Expander with Dropstuff/Expander Enhancer (Mac), or Winzip (Windows) to open the archive. Then open the file SPdbVTut.html with your browser and proceed.

133. RasMol Tutorial http://www.usm.maine.edu/~rhodes/RasTut/

Click here to view an older version of this tutorial without frames. At the end of each section, click the link for the next section.

134. File Has Moved This file has moved to http//www.ch.cam.ac.uk/SGTL/. http://www.ch.cam.ac.uk/SGTL/home.html

This file has moved to: http://www.ch.cam.ac.uk/SGTL/

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