Transcript Kinemage; Rasmol and Chime C371 Chemical Informatics Kinemages • kinemage (kinetic image) • View structure for which the coordinates have already been determined • size.

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.h
tm
• 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