1. Kinemage; Rasmol and Chime C371 Chemical Informatics

2. Kinemages kinemage (kinetic image) View structure for which the coordinates have already been determined size of the structure limited by the number of vectors needed to describe the molecule Included with the journal Protein Science http://www.faseb.org/protein/

3. Kinemage Where to obtain software: The Richardsons’ 3D Protein Structure Laboratory and Kinemage Home Page http://kinemage.biochem.duke.edu/ – Mage: display kinemages –Prekin: makes them for molecules –Java Mage: http://kinemage.biochem.duke.edu/javamage/java.html

4. RasMol Created by Roger A. Sayle RasMol – RASter Display of MOLecules Gale Rhodes’ Tutorial: http://www.usm.maine.edu/~rhodes/RasTut/index.html

5. RasMol 2.7 Renders each atom in its specified 3-D position according to the data in an atomic coordinate file Adds the appropriate covalent bonds Interprets data: –atoms, secondary struture, disulfide bridges, hydrogen bonding, polypeptide chains, etc.

6. Rasmol 2.7 Uses a specialized command language Available for Windows, Macintosh, Unix, VMS, Linux Open-Source Software Reads: –PDB, Mol2 (Tripos), Mol (MDL), XYZ (XMol), CHARMM, CIF, mmCIF

7. Rasmol 2.7 Writes raster or vector PostScript PLUS: –GIF, PPM, BMP, PICT, Sun rasterfile, MolScript, Kinemage, RasMol, PDB Forms the basis for other programs, such as WebLab Viewer and Chime

8. RasMol Molecular Visualization Freeware ("RasMol") Email List http://www.umass.edu/microbio/rasmol/raslist.htm How to obtain RasMol: http://www.umass.edu/microbio/rasmol/getras.htm#rasmanual

9. Deep View (Swiss PDB Viewer) Gale Rhodes’ Tutorial http://www.usm.maine.edu/~rhodes/SPVTut/index.html

10. Chime Chime: CHemical mIME Developed by MDL Information Systems –http://www.mdli.comhttp://www.mdli.com Supports true animation

11. Chime: How it Works: How Chime Works by Eric Martz http://www.umass.edu/microbio/chime/chimech.h tm Encodes internally Chemical MIME types

12. 3D Chime Figures from Crystal Data Royal Society of Chemistry Journals: http://www.rsc.org/is/journals/authrefs/3dfigures. htm

13. Chime: Problems with IE Microsoft removal of support for the plug-in interface (MS IE 5.5 SP2 and higher) MDL working to make Chime independent of browser technologies

14. Chime Demo Sites World Index of Molecular Visualization Resources http://molvis.sdsc.edu/visres/ Liz Dorland’s Chemistry Tutorial and Resource Page http://www.mc.maricopa.edu/academic/phy_sci/Chemistry/faculty/dorland/chime.html Chime Resources by Eric Martz http://www.umass.edu/microbio/chime/

15. Chime: Where to Get It: From MDL: http://www.mdlchime.com/chime/

16. Other Sites SIRCh: Molevular Visualization Tools & Sites http://www.indiana.edu/~cheminfo/mvts.html