SIRCh :: Molecular Visualization Tools & Sites

XMView at the Indiana University Molecular Structure Center (will generate publication quality molecular graphics. Available for Red Hat Linux and SGI workstations)

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Chemical MIME

Chemical Object Test Page at LLNL (includes information needed to configure browsers for chemical MIME types)
The MIME Types

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Free Viewer and Plug-in Software

Chemscape Chime (MDL) (includes examples and tutorials; see below for others)
- Demonstrations for Chime/Chime Pro 2.0
- Molecules in four dimensions (Mol4D)
- Chime RasMol Scripting Tutorial at MDL
- Exercises in Point Group Symmetry by Arie Aizman
- Liz Dorland's Chemistry Tutorial and Resource Page (includes: "WWW Chemistry Tutorials Using the Chime Plugin")
- Molviz.org, Molecular Visualization Resources collected by Eric Martz (Unive rsity of Massachusetts, Amherst)
- MDL Chime as a JCAMP-DX Data Viewer for Windows (for spectra)
World Index of BioMolecular Visualization Resources
RasMol Home Page
CambridgeSoft's ChemDraw Net
Cosmo VRML viewer
DS ViewerLite (formerly, WebLab ViewerLite) NO LONGER AVAILABLE FREE
Jmol
JCamp-DX Data Viewer for Windows (for spectra)
Mage Software for Macintosh, PC, Linux and UNIX Platforms
The Richardsons' 3D Protein Structure Laboratory and Kinemage Home Page
JSpecView Applet Specification
OpenRasMol Home Page
RasMol Manual
Molecular Visualization Freeware: Protein Explorer, Chime & R asMol (RasMol Home Page)
ChemDraw Viewer (CambridgeSoft)
ChemSketch (ACD Labs)
Structure Drawing and Reporting - ChemWindow (BioRad)
Cn3D (NCBI's free viewer for Entrez)
Swiss-Pdb Viewer
- Swiss-Pdb Viewer Tutorial
- Molecular Modeling for Beginners: T utorial for Deep View (Swiss-Pdb Viewer) (Gail Rhodes)
ISIS/Draw(Elsevier MDL)
3D Macromolecule Analysis and Kinemage Home Page at the Richardso n Laboratory (Mage Software for Macintosh, PC, Linux and UNIX Platforms)
Moviemol, An Easy-to-Use Molecular Display and An imation Program
pyMOL

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Selected Commercial Products

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Molecular Rendering Software

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Visualization Demonstration Sites

World Index of Molecular Visualization Resources by Eric Martz and Trevor D. Kramer
Molecular Models in .pdb Form by Dr. Dave Woodcock
Protein Science Kinemages
Demonstrations for Chime/Chime Pro 2.0
NCI-3D Database via Chemscape (Requires Netscape Navigator, Chime, and ISIS/Draw)
Chemist's Art Gallery
Structural Biology Collection (Theoretical Biophysics Group, Beckman Institute, UIUC)
Common Molecules Collection (Indiana University Molecular Structure Center Reciprocal Net Project)
History of visualization of biological macromolecules by Eric Martz and Eric Francoeur
Chemical Object Test Page at Lawren ce Livermore National Laboratory
C4: Computers in Chemistry at Cabrillo College (includ es a Chime Tutorial)
WebMolecules: site designed for the 3D visualization of molecules.
ChemVis
Molecular Database without Transi tion Elements; Banque de molécules et d'ions ne contenant pas d'éléments de transition (by Gerard Dupuis)
MathMol Library of 3-D Molecular Structures

NCI-3D Database via Syncon
NCI-3D Database via NIH Specialized Information Serv ices
ChemVIZ (Chemistry Visualization Program at NCSA)
mineral web
Virtual Museum of Minerals and Mole cules
Molecular Biophysics Images (Theoretical and Computational Biophysics Group, UIUC)
Molecule of the Month
Flick Coleman's Chime s te at Wellesley

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GIF Depictions

ChemWindow (BioRad)
GIF/PNG-Creator for 2D P lots of Chemical Structures

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Java and Javascript

Java Chemical Sample 3D Molecule Structure Viewer (John Purvis, Pomona College)
ChemApp, the Chemical Sample Viewer
Chemical Markup Language (CML)
Jmol (for Windows, Mac OS X, and Linux/Unix systems) The JmolApplet is a web browser ap plet that can be integrated into web pages. The Jmol application is a standalone Java application that runs on the desktop. The JmolViewer is a development tool kit that can be integrated into other Java applications.
- Jmol Documentation
JME Molecular Editor (Java applet to draw or edit molecules and reactions, including generation of substructure queries, and to depict molecules directly within an HTML page. Editor can generate SMILES or MDL mol file of created structures.)
JaMM at the Indiana University Molecular Structure Center
Marvin Java applets

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VRML

Chemical Examples of VRML
VRML for the Communication with 3D Scenarios of Biomolecules
ACD's ChemSketch using the Goodies toolset available from the website (www.acdlabs.com). The goodies toolset coded in ChemBasic. The Chemsketch program includes the 2D to 3D energy minimization routine prior to exporting to VRML.
Cosmo Player VRML Plugin
VRML Resources for Chemistry
VRML File Creator for Chemical Structures Generation of VRML scenes from your 2D or 3D data files (supports over 40 structure file formats). Automatic generation of 3D coordinates if not contained in the input structure. Many display options to control the visual appearance.
OrbVis is an online service for the calculation and visualization of molecular orbitals. The service will visualize all MOs of any reseonable structure you create. It employs a combination of a VRML2.0 plugin and a JAVA1.1 applet with many display options to control the visual appearance.

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URL: http://www.indiana.edu/~cheminfo/mvts.html
Broken link? Send comments to Gary Wiggins
Last updated: 10.10.2003
Copyright 2003, Gary Wiggins

SIRCh: Molecular Visualization Tools & Sites

For lecture notes on this topic, see Chemical Information Sources Wikibook As of 1 January 2007, this page is no longer updated at this site. Consult SIRCh Wiki to find a Wiki version that is being maintained.

For lecture notes on this topic, see Chemical Information Sources Wikibook
As of 1 January 2007, this page is no longer updated at this site. Consult SIRCh Wiki to find a Wiki version that is being maintained.