Exploring 3D molecular structure with computer visualization
using MDLI's Chemscape Chime & Protein Explorer
a workshop by
, Oct 16 1999,
Augustana College, Rock Island IL
Dennis Gallo, Jr.
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)
Great Chime Sites has links to some other chemistry sites.
This is linked to their
Chime Support website.
- 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
of Biochemistry [Worth]),
or the tutorials on
Protein Secondary Structure, DNA and DNA-Binding Proteins
by Frieda Reichsman.
Driscoll's Macromolecular Structure site
which includes good coverage of protein-nucleic
- 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.
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
- Download the PDB file, or
simply note the 4-character PDB ID code.
- Explore your macromolecule(s) in the
- 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