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Kinemage; Rasmol and Chime

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

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  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.com • Supports true animation

  11. Chime: How it Works: • How Chime Works by Eric Martz http://www.umass.edu/microbio/chime/chimech.htm • 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

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