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

Kinemage Where to obtain software: The Richardsons’ 3D Protein Structure Laboratory and Kinemage Home Page – Mage: display kinemages –Prekin: makes them for molecules –Java Mage:

RasMol Created by Roger A. Sayle RasMol – RASter Display of MOLecules Gale Rhodes’ Tutorial:

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") List How to obtain RasMol:

Deep View (Swiss PDB Viewer) Gale Rhodes’ Tutorial

Chime Chime: CHemical mIME Developed by MDL Information Systems – Supports true animation

Chime: How it Works: How Chime Works by Eric Martz tm Encodes internally Chemical MIME types

3D Chime Figures from Crystal Data Royal Society of Chemistry Journals: 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 Liz Dorland’s Chemistry Tutorial and Resource Page Chime Resources by Eric Martz

Chime: Where to Get It: From MDL:

Other Sites SIRCh: Molevular Visualization Tools & Sites