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 Sciencehttp://www.faseb.org/protein/

Kinemage

• Where to obtain software:• The Richardsons’ 3D Protein Structure Laboratory

and Kinemage Home Pagehttp://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 Listhttp://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’ Tutorialhttp://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 Martzhttp://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 Resourceshttp://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 Martzhttp://www.umass.edu/microbio/chime/

Chime: Where to Get It:

• From MDL:http://www.mdlchime.com/chime/

Other Sites

• SIRCh: Molevular Visualization Tools & Siteshttp://www.indiana.edu/~cheminfo/mvts.html