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Kinemage; Rasmol and Chime. C371 Chemical Informatics. 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
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Kinemage; Rasmol and Chime C371 Chemical Informatics
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/
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
RasMol • Created by Roger A. Sayle • RasMol – RASter Display of MOLecules • Gale Rhodes’ Tutorial: http://www.usm.maine.edu/~rhodes/RasTut/index.html
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.
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
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
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
Deep View (Swiss PDB Viewer) • Gale Rhodes’ Tutorial http://www.usm.maine.edu/~rhodes/SPVTut/index.html
Chime • Chime: CHemical mIME • Developed by MDL Information Systems • http://www.mdli.com • Supports true animation
Chime: How it Works: • How Chime Works by Eric Martz http://www.umass.edu/microbio/chime/chimech.htm • Encodes internally Chemical MIME types
3D Chime Figures from Crystal Data • Royal Society of Chemistry Journals: http://www.rsc.org/is/journals/authrefs/3dfigures.htm
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
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/
Chime: Where to Get It: • From MDL: http://www.mdlchime.com/chime/
Other Sites • SIRCh: Molevular Visualization Tools & Sites http://www.indiana.edu/~cheminfo/mvts.html