Most Useful Resources:

RasMol ( FREE, easy to use desktop Molecular Viewer, widely adopted, many sites and structures; Shallow learning curve, Instructions, Complete documentation, Downloadable: Windows, Mac and UNIX, ver. 2.5 and 2.6 Beta) SEE: Graphics and Animations; Data Bases for examples.

• RasMol Homepage University of Massachusettes RasMol Home page, downloading site, extensive information and examples. Also, information on Chemscape, a Chime plug-in for On-Line viewing.
• RasMol applied to VSEPR UC Berkeley examples using RasMol to examine VSEPR models.
• RasMol used in illustrating Amino Acids Structures of the common twenty amino acids for viewing.
• RasMol Introductory Chemistry Assignment Molecular Visualizations and the Chemistry of Smell UC Berkeley.
• Tutorial: Using RasMol Scripts with Chime How to use Chime and RasMol in a document.

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MDL Chemscape Chime (FREE Plug-in Viewer: Windows and Mac. SEE Topics: Graphics and Animations; Data Bases for additional examples.)

Chime Tutorial Harry Ungar, Cabrillo College, C4 Project: Excellent tutorial. For examples, downloads and more see Homepage.10/97
Chime Student Exercises includes sets of organic chemistry problems incorporating Chime models.  1/99
• Chime html Illustrations Eric Martz: Examples of using the basic Chime features.  4/97
• Chime Frames Illustrations Eric Martz: Examples and a How to for using Chime with frames. 4/97
• Chime Java Illustrations Eric Martz: Examples of Chime and Java script. (Downloadable script examples and links to key Java descriptive pages.) 4/97
• MDL ChemScape Chime FAQ ChemScape information and answers from MDL.
• Chime-Plugin(General information on Chime/ChemScape from Oxford University with examples.)
• Beginner's Guide to Chime (A basic set of user instructions.)
• Hyperactive Molecules Using Chemical MIME A description of Chemical Mime with links and examples from project co-leader Prof. Henry Rzepa, Imperial College London.
• MIME types for Chemistry A description of Chemical Mime with links and examples from project co-leader Prof. Benjamin Whittaker, Leeds College.
• Random Java Script Excellent interactive tutorial with chemistry questions on randomized molecular structures from Oxford University.
• Virtual Student Model Kit Excellent examples from Western Washington University. 
• Chemscape Chime Examples A wide range of different examples from MDL.

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MSI's WebLab ViewerLite (Free Viewer: Windows and Mac.) Lacks detailed instructions, but program is fairly intuitive with excellent images and features such as providing bond lengths, bond & torsional angles and charge densities. Can display ISIS Draw files and also add hydrogens to the displayed molecule.
                http://www.msi.com/solutions/products/weblab/viewer/register/lite/download_lite.html

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(MDL's) ISIS Draw and Add-ins (FREE to educators and students for home use: 2-dimension Chemical Structure Drawing Program: Windows and Mac). Latest version has the feature of generating files that can be viewed in 3-d with Chime and/or RasMol. (Structures are not minimized and hydrogens are not included in visualizations.)

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ACD's ChemSketch (FREE Chemical Structure Drawing Program: Windows and Mac)

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Bio-Rad / Softshell's ChemWeb (FREE Chemical Structure Drawing Program: Useful for Net ONLY, saves structures as gif files...Mac and Windows.) See also Freeware List of various Softshell programs.

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CS ChemOffice Net (FREE Subset of ChemDraw and Chem3D For Net Use ONLY; Can be used with ChemFinder and Other Web Sites)

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Babel (A File Format Interchange Progr am from Pat Walters and Matt Stahl at the University of Arizona.)

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National Center for Biotechnology Information (NCBI) free viewer: Cn3D. Designed explicitly for use with the MMDB: Molecular Modeling Database A complete, updated version of the Brookhaven Protein Database in ASN.1 improved format. Viewer does not handle .pbd format.

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General Background Information on Modeling:

MathMol (Mathematics and Molecules: a starting point for the introduction to molecular modeling from New York University.)

Intoduction to Molecular Modeling (A thorough mathematical and conceptual treatment from Georgia State University). Student Exercises:Undergraduate and Graduate Exercises (Various exercises: General Chemistry, Organic and Advanced Organic using PC Model but applicable to any modelling program.)

Molecular Modeling and M.O. Theory (A course of six lectures and one problem solving session from Prof. Henry Rzepa, Imperial College, London.)

Computational Chemistry & Molecular Modeling(A course on molecular file building using MOPAC, Gamess and other formats: aimed at synthetic organic chemistry from Hens Borkent, CAOS/CAMM Center, Univ. of Nijmegen, the Netherlands.)

Representation of Molecular Models (A description of the different techniques used to develop 3-dimensional molecular renderings.)
 
 


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List of Viewers (with links) (Extensive List with notations on ease of use with with GAMESS output. Developed by the Gordon Group of Iowa State University)
 
 

List of Molecular Modeling Programs and Developers (Comprehensive List maintained by Silicon Graphics Systems for Chemistry and Biotechnology.)

List of Computational Software Sites and Programs (Includes various builders and viewers from the Computational Chemistry List.)

Short List of Viewers Protein and Nucleic Acid Resource Manager (Temple University.)

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Select Pointers to many other programs and applications:

• CAOS/CAMM Center Univ. of Nijmegen, the Netherlands, Resources for molecular modeling and apllications to organic synthesis.
• CCMS Home Page (San Diego Supercomputing Centers: Computational Center for MacroMolecular Structure, provides a Java molecular viewer: ColorFigures and Java Molecular Viewer .)
• Chem-edit Download FREE drawing program (Macintosh).
• Corina Moleucular buider useful for generating 3-D coordinates of "drug size" molecules including rings.
• Flex Molecular graphics program. Displays 3D ball-and-stick models using Xwindows for workstations. Can animate PDB data.
• HMO-plus This Macintosh program allows the structure of a molecule to be drawn with the mouse by selecting any desired rings or heteroatoms from a palette. Export/import to connection table. Also does molecular orbital calculations.
• KineMAGE MAGE Program (for Macintosh and Windows) is distributed by the journal Protein Science to visualize [protein] structures.
• MacMolecule 1.7 Download a Macintosh program designed for creating 3D-images of molecules (requires a 68K FPU or softFPU). A new derivative for Beta testing: MacMolecule 2.
• MicroWorld is a molecular display and analysis program for the Macintosh. It calculates three dimensional models (Lines, Dreiding, Ball&Stick, Space Fill) from 3D atom coordinates, e.g. from x-ray data, 3D-databases, publications or other chemistry software.
• MMII Download FREE Macintosh molecular structure display and query/optimization program.
• Moledit Create and edit MOPAC input files (DOS and Windows).
• MolView A Macintosh program for viewing molecules(Previously called MacInPlot).
• Molviewer 3D molecular viewer (NeXTStep Application).
• Molecular Monte Carlo Monte Carlo calculations can be used to predict thermally-averaged structures, molecular charge distributions, reaction rate constants, free energies, dielectric constants, compressibilities, heat capacities, phase transition temperatures...just about anything. (GOOD starting resource with links.)
• Molecular Simulations Inc Molecular Simulations Inc. Biosym and other product information
• PDB2POV SGI, Macintosh, and Amiga: pdb file viewer of ray-traced, realistic 3-D images generated with POV Ray Tracer FREE.
• Xmol 3D X-windows program for viewing molecular structures.
• WebLab (A RasMol Derivative.)

 

 

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