Crystals, X-rays and Proteins

Comprehensive Protein Crystallography

by D. Sherwood and J. Cooper [1], [2].

Oxford University Press (2010, 2015)

ISBN: 019955904X

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 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...
Chemistry World
Crystallography Times
Crystallography Reviews
Acta Crystallographica D

Derivation of vector triple product equation (supplementary material for Chapter 2, page 41): click here.


Coordinate transformations (supplementary material for Chapter 15, page 588): click here.


Reciprocal cell parameters, d-spacings, angles between lattice planes and zones / directions (general supplementary material for Chapter 8): 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: ic50.org.uk/gencrycal
Crystallographic coordinate transformation tool: ic50.org.uk/fractorth
CIF to PDB file converter: ic50.org.uk/ciftopdb
Analyse dose-response curves: ic50.org.uk and ic50.tk
Probability tree drawing tool: ic50.org.uk/probabilitree
Parametric coil drawing tool: ic50.org.uk/crystalcurls
2D Voronoi polyhedra animation tools: ic50.org.uk/voronoi.html, ic50.org.uk/voronoia.html, ic50.org.uk/voronoid.html and ic50.org.uk/voronoi_vexer.html
Michaelis Menten Plotly tool: ic50.org.uk/kmvmaxly
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.