Errata for the revised paperback (2015) edition
The most important ones
p. 302, line 1, replace 'be can' with 'can be'.
p. 588, 3rd para, line 1, replace 'important the check' with 'important to check'.
Chapter 3. It should have been stated that with triclinic unit cells, the convention is for all angles to be acute, though the convention allows for two possibilities: all acute or all obtuse. Thanks to Dr Ian Tickle (Global Phasing) for making this point.
Typographical / stylistic - i.e. the least important ones
Ditto for pages 444, 445 and 446 where all of the 1/2's should be formatted better.
Errata for the hardback (2010) edition
The most important ones
Significant
p. 422, Figure 11.28 should have been drawn with a more obviously equal to b like this this since the cell is tetragonal.
Others
p. 132, under 'Pain...' in 'Bibliography' indent 'Both these books...'.
p. 183, under 'Papoulis...' indent 'Both these books...'.
p. 228, Fig. 7.4 legend. The alpha in the formula should be a 'proportional to' symbol.
p. 302, line 1, replace 'be can' with 'can be'.
p. 402, paragraph 2, line 5: Space between "Fig." and "11.23" is too large.
p. 418, third to last line: Space between "equation" and "(11.32)" is too large.
p. 420, paragraph 2, line -2: Space between "equation" and "(11.33)" is too large.
p. 421, between eq. (11.34) and (11.35), last line: Space between "equation" and "(11.34)" is too large.
p. 422, paragraph 2, line 5 and line -3: Space between "Fig." and "11.28(2)"/"11.28(b)" is missing.
p. 423, paragraph 1, line 13: Space between "equation" and "(14.1)" is too large.
p. 424, paragraph 1, line -1: (Parsons 2004) should be Parsons (2004).
p. 557, 5th equation: The 'T' superscript to 'X' should be plain text, i.e. not italic (as in the equations above).
p. 588, 3rd para, line 1, replace 'important the check' with 'important to check'.
p. 616, add "Rupp, B. Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology. Garland Science, New York, 2009." to 'Reference works' above 'Sanderson, M.R....'.
p. 619, add "maximum likelihood, 454, 586" to the Index above "Maxwell's equations...".
p. 619, add "model-building, 548" to the Index above "Modulus of a...".
p. 619, add "fitting, 548" to the Index term "map" just above "Fourier".
p. 619, add "occupancy, 505" to the Index above "order of reflection...".
Chapter 3. It should have been stated that with triclinic unit cells, the convention is for all angles to be acute, though the convention allows for two possibilities: all acute or all obtuse. Thanks to Dr Ian Tickle (Global Phasing) for making this point.
Many thanks indeed to Wolfgang Skala (Salzburg) for reporting most of the above points.
Please let me know of any further typos, etc, by e-mail to...
jon.cooper@ucl.ac.uk
... since I would like to keep this list updated. Thank you.
What the book reviews say...
Crystals, X-rays and Proteins - Comprehensive Protein Crystallography
D. Sherwood and J. Cooper, Oxford University Press.
ISBN: 978-0-19-955904-6
Tf (crystal) = Tf (motif) × [Tf (infinite lattice)] * Tf (shape function)] (1)
The Fourier transform of the crystal is equivalent to the FT of the motif (molecule) times the convolution of the FT of the lattice, a series of Dirac delta functions and the FT of the shape function, is all you need to know. Well not really, but if you truly understand this equation then you are a long way to understanding the principles of X-ray diffraction.
The first two-thirds of this book was like a thriller to me. Even though I knew the answer, I wanted to see how the author would address the next topic and I could not put it down. The last third did not have the same grip on me and I kept asking myself what happened - did someone else write Part III? The book is divided into three parts, but you know that already: Part I is Fundamentals, Part II is Diffraction Theory and Part III is Structure Solution.
Part I and Part II provide an integrated approach to teaching diffraction theory. The author takes the reader through crystal basics and the wave theory of electromagnetic radiation along with the mathematical tools to understand them. In Part II the authors painstakingly develop diffraction theory by analyzing one dimensional lattices then three dimensional lattices. Next the authors explore the concept of lattices with motifs and develop all the details from first principles. The latter includes the derivation of the Laue equations and Bragg's law. I found the step wise description of the Fourier transform and the effect of applying it to various functions and objects something that would help students immensely in understanding the relationship between direct space and reciprocal space.
Part III provides a description of the modern methods for protein crystallography. Much attention is spent on Patterson methods and the phase problem, with the same attention to detail as the first two parts. There is a good description of least squares refinement and the adaptions for constraints and restraints. Maximum likelihood and simulated annealing are also described. However very little about statistics is discussed. This is a very important topic in crystallography and deserves more space. I found Part III lacking in the practical aspects of modern protein crystallography although it is very well referenced.
Joseph D. Ferrara, Ph.D.
Supplementary material
Derivation of vector triple product equation (supplementary material for Chapter 2, page 41): click here .
The area under the Dirac delta function (supplementary material for Chapter 5): click here .
Reciprocal cell parameters, d-spacings, angles between lattice planes and zones / directions (general supplementary material for Chapter 8): click here .
Electron density projections (supplementary material for Chapter 9): click here .
Coordinate transformations (supplementary material for Chapter 15, page 588): click here .
Rhombohedral hexagonal setting (general supplementary material): click here .
MAID: an automated map-fitting routine, by David G. Levitt (Minnesota).
In Chapter 15, various methods for building the amino acid sequence of a protein into an electron density map are described, including several programs which attempt to do this automatically.
One such program is MAID by David Levitt at the University of Minnesota which uses torsion angle molecular dynamics as described in: "A new software routine that automates the fitting of protein X-ray crystallographic electron density maps." D. G. Levitt. (2001). Acta Crystallogr. D57, 1013-1019.
Since David's research now focusses on pharmacokinetics, with David's permission MAID can be obtained from: here .
Some other online tools that might be useful
General crystallographic calculator: here
Crystallographic coordinate transformation tool: here
Protein crystal contact calculator: here
CIF to PDB file converter: here
Analyse dose-response curves: ic50.org and ic50.org.uk
Probability tree drawing tool: here
Parametric coil drawing tool: here
2D Voronoi polyhedra animation tools: voronoi , voronoia , voronoid and voronoi vexer
Michaelis Menten Plotly tool: here
Informal essay on conic sections: cone.pdf
Electron density map viewing tool for mobile devices: minimapai.de
Beginner's guide to web scripting with lua and fengari here or here
Pattern matching in Lua cheatsheet: here .
Protein space group viewer: here and a stereo version: here
Tutorial on Octave-Symbolic: here
Tutorial on running the legacy scientific word processor for DOS: ChiWriter
