# Chemical Information Sources/SIRCh/Molecular Visualization Tools and Sites
##### Guides to Molecular Visualization Tools

* World Index of Molecular Visualization Resources
* World Index of BioMolecular Visualization Resources
* NetSci's List of Molecular Mechanics and Molecular Dynamics Software
* Universal Molecular Modeling Software list at the NIH Center for Molecular Modeling
* Interoperability and Standards
* Internet Browser Plugins and Applets for Chemists at "Links for Chemists" (Liverpool)

##### Converters of Chemical Structure Formats

* NCI/CADD Chemical Structure Resolver
* Open Babel at Sourceforge.net
* BABEL; A Molecular Structure Information-Interchange Hub
* Mol2Mol
* CLiDE (chemical literature data extraction tool from SimBioSys)
* ACD/ChemSketch
* Corina
* OSRA Optical Structure Recognition (a utility designed to convert graphical representations of chemical structures, such as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES)

##### CML and Chemical MIME

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

##### Free Viewer and Plug-in Software

* Discovery Studio Visualizer (accelrys)
* Chime (must register with Symyx)
** Molecules in four dimensions (Mol4D)
** 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)
* World Index of BioMolecular Visualization Resources
* RasMol Home Page
* OpenRasMol Home Page
* RasMol Manual
* Molecular Visualization Freeware: Protein Explorer, Chime & RasMol (RasMol Home Page)
* ChemDraw ActiveX/Plugin Net (CambridgeSoft)
* Cosmo Player VRML Plugin
* Jmol
* Jamberoo (Cross-Platform Molecular Editor)
** Jamberoo Tutorials
* JCAMP-DX (for spectra)
* JSpecView Applet Specification
* ChemSketch (ACD Labs)
* Structure Drawing and Reporting – ChemWindow (BioRad)
* Cn3D (NCBI's free viewer for Entrez)
* DeepView Swiss-Pdb Viewer
** DeepView Tutorial
* 3D Macromolecule Analysis and Kinemage Home Page at the Richardson Laboratory (Mage Software for Macintosh, PC, Linux and UNIX Platforms)
* Moviemol, An Easy-to-Use Molecular Display and An imation Program
* pyMOL

##### Selected Commercial Products

* Acorn NMR Inc. (NUTS)
* Serena Software (PCMODEL)
* Jaguar
* Spartan
* Scigress Explorer (previously, CAChe)
* HyperChem

##### Molecular Rendering Software

* Corina
* CACTUS (The CADD Group's Cheminformatics and User Tools at NIH NCI)
* PDB3D: Realtime 3D Molecule Renderer for the WWW
* Molecules in four dimensions (Mol4D)
* The WWW PovChem Manual (Paul Thiessen)
* VMD: Visual Molecular Dynamics
* gOpenMol
* GIF/PNG-Creator for 2D Plots of Chemical Structures
* XMView at the Indiana University Molecular Structure Center (will generate publication quality molecular graphics. Available for Red Hat Linux and SGI workstations)
* Jmol (for Windows, Mac OS X, and Linux/Unix systems) The JmolApplet is a web browser applet 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

##### Visualization Demonstration Sites

* Chemist's Art Gallery
* Molecular Biophysics Images (Theoretical Biophysics Group, Beckman Institute, UIUC)
* History of visualization of biological macromolecules by Eric Martz and Eric Francoeur
* Chemical Object Test Page at Lawrence Livermore National Laboratory )
* WebMolecules: site designed for the 3D visualization of molecules.
* ChemVis
* Molecular Database without Transition 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 NIH Specialized Information Services
* ChemVIZ (Chemistry Visualization Program developed at NCSA)
* Virtual Museum of Minerals and Molecules
* Molecular Biophysics Images (Theoretical and Computational Biophysics Group, UIUC)
* Molecule of the Month
* Flick Coleman's Chime site at Wellesley

##### VRML

* VRML Resources (Education Center on Computational Science and Engineering, San Diego State University)
* Virtual Reality Modelling Language (VRML) in Chemistry
* 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 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.