VISITS
Understanding X-ray
Crystallography
Workshop for Users of the
Small-Molecule X-Ray Diffraction Center At
Colby College
Last revisions 2003/07/23, 10:30
PM.
Gale Rhodes
Department of Chemistry
University of Southern Maine
9:00 AM - 3:30 PM
Thursday, July 24, 2003
Miller Library (same location as last year)
Davis Educational Foundation Electronic-Research Classroom
Colby College
Map of the
Colby Campus
Overview
Almost anyone can now solve structures using crystallographic
instruments and software as black boxes, more or less the way you
drive your car. My main focus in this workshop is to enhance your
understanding of what's going on under the hood in crystallography,
which makes it more likely that you can figure out what's wrong when
your structure determination is not going well.
Crucial to understanding crystallography is getting a feeling
for the relationship between diffraction patterns (the data of
crystallography) and the crystal and molecular structure that
produces the diffraction pattern. As a great visual aid in this
endeavor, we will use the Interactive Structure Factor Tutorial, part
of Kevin Cowtan's Book of Fourier.
You'll get more out of this workshop if you read the Suggested
Reading before you come. The little book by Clegg is about as
lightweight as crystallographic books get, but it's still
challenging. You'll have ample opportunity to ask questions about
this book and all other topics I plan to discuss. The Book of Fourier
gives you a chance to play with some software that teaches the
relationship between diffraction data and the structure of molecules
in crystals. We will play with it more during the workshop.
Suggested Readings (before workshop)
- Crystal Structure Determination, William Clegg, Oxford
Science Publications, 1998. A very concise introduction.
- Kevin
Cowtan's Book of Fourier Interactive tools for
understanding the fourier transform, the mathematical heart of
crystallography.
A Useful Reference (after workshop)
- Crystal Structure Determination, Werner Massa,
Springer-Verlag, 2000.
Both books will be provided to each
participating school.
Workshop Schedule
9:00 AM - Assemble
- Coffee, tea, juice, muffins, bagels, and other essentials
9:30 AM - Getting Started
- Introductions
- Why Do Crystallography?
- Brief Overview of Crystallography (see Clegg's flowchart,
Figure 2.1, page 27)
10:30 AM - Coffee Break
10:45 AM - From Diffraction Pattern to Model
- Physical Meaning of the Fourier Transform
- Bragg's Law, Miller Indices, and Diffraction Patterns
- Structure Factor: A Mathematical Description of a
Reflection
- From Structure Factors to Electron Density
- The Phase Problem
12:00 Noon - Lunch
1:00 PM - Phasing, Refining, Interpreting
- Finding Phases: Patterson Methods, Direct Methods, and Brute
Force
- Refining the Model
- Judging Model Quality (see this Glossary
of terms)
- What Does the Model Mean?
2:15 PM - Break
2:45 PM - Small-Molecule X-ray Diffraction Center at Colby
College
- Brief reports from users of the Center
1. Rebecca Conry, Colby: New Structures and Aspects of the
Solutions
2. Other users, TBA
- Resources for users
3:00 PM - Crystallography in the Curriculum at Consortium
Schools
- Brief reports from consortium faculty
1. Rebecca Conry, Colby: Some Ideas and Suggestions
2. Gale Rhodes, USM: Growing
Protein Crystals: A Biochemistry Lab Experiment at
USM
3. Others, TBA
- Resources for teachers
3:30 PM - Adjourn
Resources
- Instructions for using the Center
- Descriptions of Instruments
- Links to crystallographic resources
- Interactive tools for understanding the fourier transform, the
mathematical heart of crystallography.
- An excellent online introduction to x-ray crystallography,
including many interactive learning tools.
- More interactive learning tools.
- Software for simulating data collection and processing.
- Lab projects using Bruker equipment and software. See
Journal of Chemical Education, 79, April 2002, page
420. (Thanks to Barbara Stewart of UMO for supplying this
information.)
- A glossary of terms in structure determination by
crystallography, NMR, and homology modeling
- Designed for macromolecular models, but many terms apply to
small models
- Home page for the book, Crystallography Made Crystal Clear:
A Guide for Users of Macromolecular Models
- Molecular graphics training, an outreach program for students,
teachers, and researchers
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