MolVis Workshop for MACTLAC

Exploring 3D molecular structure with computer visualization using MDLI's Chemscape Chime & Protein Explorer
a workshop by Eric Martz for MACTLAC, Oct 16 1999, Augustana College, Rock Island IL
hosted by Dennis Gallo, Jr.

If this is a paper copy, go to the on-line version at
www.umass.edu/microbio/rasmol/mactlac.htm

These Chime resources require Netscape Communicator
(Due to lack of full plugin support, Internet Explorer won't work properly!)
and MDL Chemscape Chime freeware.

Contents

Chime Basics
Micromolecules and Crystals
Spectral Animations
Macromolecules: Ready to Run Tutorials
Macromolecules: Find and Show Your Own
Ideas for Lessons

Chime Basics

Capabilities common to all Chime-based websites: Mouse and Menus.
Why Chime? RasMol vs. Chime vs. Protein Explorer.
Micromolecules and Crystals
Organic Chemistry in Chime (Dave Woodcock, Okanagan University College, BC CA)
Inorganic crystals (Andrew Maverick, Louisiana State U)
Inorganic crystal lattices "75 structures in 36 of the 230 space groups" (Young and Mehl, Naval Research Lab)
Small biochemical compounds (Washington U, St. Louis - KLOTHO)
Pharmaceutical compounds with thermal animations (Akira Dobashi, Tokyo U of Pharmacy & Life Sci, 3D Molecular Modeling Homepage)
MDLI's Great Chime Sites has links to some other chemistry sites. This is linked to their Chime Support website.
Spectral Animations
IR Spectra with Animations (Robert Lancashire, Paul Lahti et al.)
Macromolecules: Ready to Run Tutorials
Tutorials on DNA, hemoglobin, antibody, MHC are available from UMass Chime Resources.
Don't miss the tutorials on Amino Acids and Sequence and Primary Structure by Tim Driscoll (more topics coming soon to this site for Lehninger's Principles of Biochemistry [Worth]), or the tutorials on Protein Secondary Structure, DNA and DNA-Binding Proteins by Frieda Reichsman. See also Driscoll's Macromolecular Structure site which includes good coverage of protein-nucleic acid interactions.
Duane Sears offers an extensive protein biochemistry site including practice quizzes,
Ricky Cox's site emphasizes noncovalent bonds, especially pi-interactions involving aromatic rings.
Chime-based tutorials on many molecules and topics will be found in the World Index of Animated Tutorials.
An excellent collection of annotated biochemistry links, many to resources employing Chime, accompanies Stryer's Biochemistry (Freeman).
Macromolecules ("PDB Files"): Find and Show Your Own
Popular molecules are listed in PDB at a Glance (NIH, Bethesda MD)
Search all published structures with
- PDB Lite (nonspecialists should start with PDB Lite)
- or the more advanced SearchFields at the Protein Data Bank
Download the PDB file, or simply note the 4-character PDB ID code.
Explore your macromolecule(s) in the Protein Explorer.
Make a class web page of links which bring up prespecified molecules in the Protein Explorer or Comparator. Here is a demonstration page of diverse examples.
Methods for creating your own Chime tutorials are available.
Ideas for Lessons