9:30 AM Practical Crystallography: How to get started and what information does it give me. We will examine the answers to these questions and move through an active dialogue using real world examples.
Description here....
Bibliography
10:45 AM Break
11:15 AM Analysis of Three Dimensional Structure: Voronoi Polygons and Distance Geometry; Three Dimensional Imaging
As introduced on Thursday in the context of studying secondary structure, modeling can be informed by multiple perspectives. After viewing three dimensional stereo slides of biological macromolecules, we will explore how aesthetic considerations can inform our modeling approaches. In particular, we will use a result from distance geometry (Voronoi polygons and Voronoi polyhedra) to understand the nearest neighbor packing constraints of side chain residues. We will show how these can be modeled with origami paper folding, compass and straight edge drawings, and baking bread as well as with some elegant (and elementary) mathematics. We will also consider how two dimension models help us build three dimensional models.
2:30PM - 2PM Lunch
Afternoon Laboratories
2-3:45 PM Molecular Graphics: drawing packages, various molecular viewing packages, etc.
SOFTWARE: Kinemages (MacOS, Windows, Unix)
3:45 PM Break
4:00 - 5:00 PM CONCLUDING SESSION
Software:
Description: RasMol is a free program which displays molecular structure. It is available for on
PC/Windows (RasWin), MacIntosh (RasMac), unix, and VAX VMS (the latter
two via X-windows), and also (through ports by users) for NEXTSTEP. RasMol is a powerful educational tool for showing
the structure of DNA, proteins and smaller molecules in beautiful, space-filling, colored, 3-dimensional
images.
Written by: Roger A. Sayle (GlaxoWellcome & University of Edinburgh, UK)
For more information: RasMol homepage
Other handy resources:
Bookstores:
Phavanantha, Phathana. "Crystallographic Schools in Thailand and Neighbouring Countries." Chulalongkorn University, Bangkok 10330, Thailand.
Kastner, Margaret E. "Instructional Materials." Department of Chemistry, Bucknell University, Lewisburg, PA 17837.
Other Suggested Readings (not attached):
Branden, C. & Tooze, J. 1991. Introduction to Protein Sructure. New
York: Garland Publishing, Inc.
Glusker, J.P., Lewis, M., & Rossi, M. 1994. Crystal Structure Analysis
for Chemists and Biologists. New York: VCH Publishers, Inc.
Rhodes, G. 1993. Crystallography Made Crystal Clear. San Diego: Academic Press, Inc.
Crippen, G. M. and Havel, T. F. 1988. Distance Geometry and Molecular Conformation, Research Studies Press, Ltd., Somerset, England, pp viii-23.
Crippen, G. M. 1988. "Voronoi Polyhedra Site Models." Distance Geometry and Molecular Conformation, Research Studies Press, Ltd., Somerset, England, pp 407-414.
Tsai, Jerry, Gerstein, Mark, and Levitt, Michael. "Using Voronoi polyhedra in the analysis of molecular dynamics simulations of small molecules and proteins in aqueous solution." Stanford University, Department of Structural Biology.
Thornton, Janet M., Orengo, Christine M., Michie Alex, Miller, Rob, and Jones, David T. "Protein Structure Classification and Threading." Biochemistry and Molecular Biology Department, University College, Gower St., London WC1E 6BT. http://www.biochem.ucl.ac.uk/bsm/
Last modified: Thur Dec 30 19:01:47 1999