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Home > BMC Book
> Online Resources > Errata,
updates Following links from my tutorial web site to Amazon.com allows you to find best new and used prices and helps to support the educational parts of this web site. See also my recommendations. Please accept my sincere apologies for the various mistakes and inaccuracies that escaped our attention. Fortunately only few true errors have been discovered so far. Some figures have been updated or improved and can be downloaded from this page. |
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| Format: page, paragraph, line(S=sidebar C=figure caption, E=equation, B=Box, F=figure), minus means 'from bottom' | Error description (Submit a new one) | Remarks |
| Preface 1, 2, 11 | of an array can be deleted | |
| x, 1, 6 | real (projections) of molecules should be projections of real molecules | |
| xi, 5, 6 | broad and helpful should be large and helpful | |
| xii, 4, 1 | the numerous should be all the | |
| xii, 5, 17 | LBNL should be LANL | Sorry, Tom. |
| 1, 1, 7 | brief should be short | |
| 3, S, col 2, line fig 13-23 | c_hannel should be channel | |
| 5, 2, 3 | bad hyphenation, should be crystallo-graphy | or maybe not |
| 5, 2,13 | sensitive should be susceptible | |
| 5,3,4 | This not the should be This is not the | Thanks, Boaz! |
| 7, 3, 5 | may not locally represent the protein structure should be may not represent the local protein structure | |
| 8, 3, 5 | structures should be structure | |
| 11, 1-2, break | paragraph break to large | |
| 13, 4, 10 | cryocool should be cool | |
| 19, S1-4, 13 | new reference to PDBe should be added | 1. Velankar S, Best C, Beuth B, et al. (2010) PDBe: Protein Data Bank in Europe. Nucl. Acids Res. 38, D308-D317. |
| 20,4,11 | graphic should be graphics | |
| 24,5,3 | seleno cysteine should be selenocysteine | check throughout chapter 2 |
| 25, C2-1 | add reference to 2009 Nobel Prize for Ribosome before "PDB entries..." | For their work ultimately leading to the determination of the ribosome 50S subunit structure, V. Ramakrishnan, T. A. Steitz and A. E. Yonah shared the 2009 Noble Prize in Chemistry. |
| 27,1,1 | deviate should be vary | |
| 28,2,9 | As most should be Because most | |
| 29,2,2 | delete 20 | |
| 29,2,3 | The peptide bond is formed between two amino acids between should be The peptide bond between two amino acids is formed between | |
| 31, C2-9, 9 | cis should be italic cis | |
| 31,2,6 | described should be discussed | |
| 33,S2-3, 1,13 | of proteins should be in proteins | |
| 35,C2-13 | Add a remark that the PP-II helix is in the strict sense of backbone interactions not a bona fide SS element. | ...nitrogen. A PP-II helix therefore does not not comply with the strict definition of secondary structure elements via their backbone hydrogen bonding patterns. |
| 35, 3,13 | -180/+180 should be +180/+180 (the same but would be more consistent) | |
| 36,2,10 | the strands and extended should be the strands. Extended | |
| 36,3,5 | idealized should be ideal | |
| 36,F2-14 | The arrows in the right panel are inconsistent with chain direction | updated figure for download (gif) here |
| 36,F2-14 | Note to typesetter: figure 2-14 has been updated - new fig (bmp) needs to be picked up from server - do not use old figure | Thanks Tobias! |
| 39,2,8 | So far, we have not needed to pay should be So far we did not have to pay | ... |
| 40,1,9 | amino acids and proteins should be amino acid residues in proteins. | |
| 44,2,6 | by surface should be via surface | |
| 45,2,2 | the rigid should be the rigidity of the | |
| 46, F2-25 | The side chain NH2CO should be flipped for consistency with density | updated figure for download (gif) here |
| Note to typesetter: the listed figures have been updated (color scheme of annotation) - new figs (bmp) need to be picked up from server - do not use old figures | 2-20, 2-21, 2-22, 2-23, 2-24, 2-25, 2-26, 2-28 | |
| 46, C2-26, 1 | S-S double bond should be S-S bond | Thx, Manfred! |
| 47,3,3 | chain density. should be chain. | Maybe not... |
| 48,4,3 | on surface accessible proteins should be on the surface of proteins. | What was I thinking here.. |
| 52,2,5 | receptor drug should be receptor-drug | |
| 56,4,2 | It is useful as it exemplifies should be It exemplifies | |
| 56,c3-25, 1 and 3 |
motif serving should be
motif (A) serving domain of should be domain (B) of | Insert figure labels in caption |
| 62,1,1 | As we discussed should be As discussed | |
| 62,3,19 | with crystal should be with the crystal | |
| 62,3,21 | task for should be task in the case of | |
| 66,C2-43,3 and 9 |
purine bases are joined should be purin
bases (A)are joined form a nucleotide. should be form a nucleotide (B). | Insert figure labels in caption |
| 68,C2-45,10 | hydrogen donor should be hydrogen bond donor | Thx, Manfred! |
| 68,C2-45,16 | hydrogen acceptors should be hydrogen bond acceptors | Thx, Manfred! |
| 68,C2-46,12 | Zn atoms should be Zn2+ ions | Thx, Manfred! |
| 73, 2.12 Additional reading | should include reference |
1. Liljas A, Liljas L, Piskur J, et al. (2009) Textbook of Structural Biology. Hackensack, NJ: World Scientific Publishing Company. |
| 75 |
Update reference 50 |
50. Chen VB, Arendall WB, III, Headd JJ, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66(1), 12-21. |
| 78,2,1 | The following should be The remaining | |
| 79,C 3-2,6 | cheap and should be cheap, and | |
| 80,2,8 | In contrast, polycrystalline material contains a randomly oriented sample of many thousands of tiny microcrystals.. should be | In contrast, polycrystalline material contains many thousands of tiny, randomly oriented microcrystals.. |
| 82, S3-3,5 | just in crystals should be just as in crystals | |
| 83,3,6 | the limited power of global descriptors to pinpoint local properties. should be | the insensitivity of global descriptors regarding local errors. |
| 86,3,3 | < 95% should be > 95% | Thx, Manfred! |
| 87,3,5 | salt in should be salt-in | inconsistent throughout text |
| 88,1,15 | Finally, all kinds should be Finally, various kinds | |
| 90,3,12 | range 25-150 should be range of 25-150 | |
| 92,1,6 | also, unfortunately, common protein-rich should be also, unfortunately common, protein-rich | |
| 94,1,12 | or for other kinetic reasons should be or for other, kinetic, reasons | |
| 95,1,5 | inspection. should be inspection of the diffraction pattern. | |
| 95,2,2 | where it reaches should be where the solution reaches | |
| 96, 1, 4,5 | Salting-in, salting-out need consistent hyphens | inconsistent throughout text |
|
96, E 3-5 |
Typesetting error, correct equation: |
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| 97, 3, 1 | (S) should be without parenthesis S | |
| 98, 2, 1 | magnitude should be multitude | |
| 98, 4, 4 | used should be useful | |
| 101, 4, 1 | is just to mix should be is to just mix | |
| 104,4,1 | paragraph should start with bold Clear drops. | |
| 105, S3-10, -12 | of 50 ml should be of 50 µl | microliter |
| 105,2,2 | directly to create should be to immediately create | or instantaneously ? |
| 111, 3, after last sentence | after ...control experiments. , add: It has been proposed that the change in cocktail composition due to addition of seeds stock may also be a contributing factor towards increased crystallization successx. Reference x: |
X. St John FJ, Feng B, & Pozharski E (2008) The role of bias in crystallization conditions in automated microseeding. Acta Crystallogr. D64, 1222-1227. |
| 112, B 3-7, 1 | any conditions should read the exact conditions | |
| 113, S3-13, 9 | aliquots followed by protein addition with a single needle dispenser suffices should be | aliquots, followed by protein addition with a single needle dispenser, suffices |
| 114,2,9 | drop the 'all' | |
| 115, C3-34, 4 | The large cube should be the larger, green cube | |
| 115, last paragraph |
last paragraph Full factorial designs. The second sentence
contains various mistakes and should be
replaced as follows: ...factors.88 For a 2-level, 4-factor full factorial design, 16 experiments are required, and we can interpret our grid screen experiment (pH, PEG) as a simple 2-factor experiment with 6 (pH) and 4 (PEG concentration) levels resulting in 24 combinations. However... | Thanks Wolfgang for pointing this out! |
| 117, C3-35, -3 | toward soluble should be toward highly soluble | |
| 120,3,10 | drop the 'only' | |
| 123,6,2 | glossarize IC50 in this line and the definition of IC50 should go into Glossary -> |
half maximal inhibitory concentration (IC50) A measure of the effectiveness of a compound or drug in inhibiting biological or biochemical function. Quantifies how much of a particular drug or inhibitor is needed to inhibit a given biological process (such as enzyme or receptor activity) by half. |
| 124,2,3 | occupation should be occupancy | |
| 124,2,5 | occupanc should be occupancy | |
| 124,C3-40,8 | occupation should be occupancy | |
| 127,1,3 | the radical should be radical | |
| 127,1,12 | cooling also should be cooling | |
| 131,2,3 | mAbs should be mABs | |
| 139, ref 87 | Add issue number 254(23) | |
| 139, refs 99-102 | 101 and 102 are identical to 99 and 100, respectively | Needs complete renumbering of references in body text past 100 |
| 148,C4-3,-3 | as much as a single should be as little as a single | |
| 154,3,-5 | two times result - resulting | needs rephrasing by native |
| 154,SB4-3,2 | Targeted mutagenesis of should be Mutagenesis of specific | |
| 157,1,2 | PCR (using should be PCR (epPCR, using | |
| 157,1,-4 | mutation mutants should be mutation | ... |
| 159, FC4-11,4 | E. coli should be Y. pestis | |
| 160,S4-4,14 | tools in these bacteria is smaller. should be tools available for these bacteria is limited. | |
| 162,1,3 |
various codons or strains should be various codon-optimized strains or strains | |
| 162,2,4 | up to 1/10 should be up to ten times | ... |
| 167,5,3 | the stationary Ni should be the Ni | |
| 168,1,-4 | plus should be with, parenthesis removed | with.....site flows maybe.... |
| 170,C4-14,5 | Aequoria victoria should be Aequorea victoria | Thx, Wolfgang! |
| 171,3,5 | BL843(DE3) should be B834(DE3) | Thx, Wolfgang! |
| 171,3,-3 | partial occupation should be partial substitution | add residue substitution matrix in Appx |
| 191, in Additional reading | add reference no 7 |
7. Aricescu AR, Assenberg R, Bill RM, et al. (2006) Eukaryotic expression: developments for structural proteomics. Acta Crystallogr. D62(Pt 10), 1114-1124. |
| 193, refs 83 and 90 | refs 83 and 90 de Marco are identical | All refs in text past 83 need to be renumbered |
| 197,3,9 | material properties should be materials | |
| 197,3,11 | prote_in should be protein | |
| 201,3,4 | In the should be In our | |
| 203,F 5-7 | Origin in left panel should not have a ' | who put that in ? NOT in original figure - updated figure (gif) can be downloaded here |
| Typesetter: new updated figure 5-7 (bmp) needs to be picked up from server - do not use old figure. | Might have been confusing - has been updated. | |
| 203,2,1 | paragraph should be headed by bold Limitations imposed on symmetry operations. In periodically... | |
| 204,B5-3,6 | all rotation should be all crystallographic rotations | |
| 204,3,-3 | cell constants should be cell parameters | this is debatable, but serves consistency |
| 205,F5-10b | Origin of cell should be moved to red dyad for both different cell and different origin | updated figure 5-10_b (gif) can be downloaded here. |
| Typesetter: new updated figure 5-10_b (bmp) needs to be picked up from server - do not use old figure. | improved for clarity | |
| 206,3,9 | case) one should be case) of one | |
| 208,F5-15 | Add the hexagonal unit cell in blue lines to emphasize the same unit cell volume and relation to asymmetric unit. | updated figure 5-15 (gif) can be downloaded here. |
| Typesetter: new updated figure 5-10_b (bmp) needs to be picked up from server - do not use old figure. | improved for clarity | |
| 208, C5-15,end | Add: The blue outlined unit cells are equivalent in area (volume) and contents to the standard unit cell defined by the vectors a and b. | there is nothing wrong as it is but I think this addendum makes it even clearer. |
| 209, C5-16,-2 | the trigonal unit cell should be the equivalent trigonal unit cell as shown in blue in Figure 5-15 | |
| 213,S5-2,col1,-1 | isolated \greekbeta-strand should be isolated greekbeta-structure | |
| 213,S5-2,col2,2 | this \greekbeta-strand is should be these \greekbeta-strands are | |
| 213,C5-21,6 | the \greekbeta-strand should be the \greekbeta-structure | |
| 213,C5-21,7-8 | this \greekbeta-strand should be these \greekbeta-strands | |
| 213,1,1 | "near" perfect should be near-perfect | |
| 214,1,-1 | the resulting should be the corresponding | |
| 216, second paragraph from bottom, -1 | Sentence should end with thus (3 -1 -1). | remove the 31bar1bar. |
| 222,F5-34 | one visible line is drawn invisible | updated figure 5-34 (gif) can be downloaded here. |
| Typesetter: new updated figure 5-34 (bmp) needs to be picked up from server - do not use old figure. | ||
| 224,4,2 | to operator should be to the trivial symbolic operator | |
| 224,symbolic operators and matrix | Both the symbolic operator (2) and the matrix R3 are mistyped.... | updated operators and matrices can be downloaded here. Thx, Jonathan! |
| 228,4,-4 | parallel but should be parrallel to but | |
| 230,1,7 | all m positions should be all M positions | |
| 230,2,1 | "positions" should be "Positions" | |
| 230, operator 4. |
4. should be 4.
 | Copyediting error? - correct in original MS |
| 231,8,2 | (3200/42000 PDB entries) should be replaced with (Figure 5-44) | |
| 232,C5-42, end | contacts. should be contacts of an individual molecule. | |
| 233,C5-43,-2 | The odd degree signs are rubbish (already squawked in proof). Should be | become (b·cosγ, b·sinγ, 0) = b·(-0.5, 0.866, 0). |
| 233, E5-4 |
(5-4) should be | X and x are swapped..darn |
| 235,1,3 | equal. should be even. | |
| 236,1,1-2 | remove the statements (+1 DoF of rotation) and (point group n22......rotation) | The parentheses statements are confusing in absence of further explanation |
| 238,1,-1 | (31). should be (3 1). | needs a space |
| 243,2,3 | around the origin should be moved between infinite) and of | infinite) around the origin of |
| 243,3,3 | interpretation of should be construction rules for | |
| 249,F6-2 | add a logarithmic frequency axis (cf Atkins) | updated figure 6-2 (gif) can be downloaded here. |
| Typesetter: new updated figure 6-2 (bmp) needs to be picked up from server - do not use old figure. | ||
| 249,B6-1,-3 | diffraction X-rays should be diffraction of X-rays | |
| 249,B6-1,-5 | allows the use of the should be allows using the | probably better? |
| 249,B6-1, second eqn. | second equations for frequency ν needs to be inverted, should be ν = c/λ | Thx Wolfgang! |
| 251,C6-3,-6 | of electric should be of the electric | Thx Wolfgang! |
| 252,2,-3 | see)of should be see) of | Thx Wolfgang! |
| 253,2,-1 | Figure 6-6 should be Figure 6-5 | |
| 255,-2,2 | though expansion should be through expansion | Thx Wolfgang! |
| 255,S6-3, above last equation | in mathematics, should be in mathematics, the Euler Identity | |
| 255, S6-3, last equation | The Euler Identity has the wrong sign |
replace formula with correct one:
Thx, Robert! |
| 256,F6-8 |
needs to be replaced with new figure 6-8 Typesetter: new updated figure 6-8 (bmp) needs to be picked up from server - do not use old figure. |
gif here, new original on server after Sept 30th |
| 256,C6-8,4 | incoming and scattered should be scattered and incoming | |
| 256,C6-8, end | add after end of caption: The reason for assigning the scattering angle units of 2θ becomes obvious once the diffraction of X-rays is interpreted as reflection on lattice planes (Figure 6-15). | |
| 256,3,3 | First, should be Either | |
| 257,2,3 | orbits should be orbitals | Thx, Andy! |
| 257,F6-10 | Typesetter: revert to original figure 6-10 (bmp) - pls do not change aspect ratio. | Somehow the aspect ratio changed - atom is an ellipsoid. Download from gallery. |
| 258,F6-11 |
needs to be replaced with new figure 6-11 Typesetter: new updated figure 6-11 (bmp) needs to be picked up from server - do not use old figure. |
gif here, new original on server after Sept 30th |
| 259, e6-13 |
drop the FS in the beginning | gif here |
| 259,2,1 | FS should be fS | Thx, Andy! |
| 259,first bullet,1 | FS should be fS | Thx, Andy! |
| 259,first bullet,2 | FS should be fS | Thx, Andy! |
| 259,first bullet,3 | delete which is anotated as fS | Thx, Andy! |
| 259,S6-4,-2 |
The exponent misses the B-factor, should
be
 | This was correct in MS and copyedits. Grrr... |
| 259, bullet 4 | after atomic volume, the sentence should continue atomic volume, it is convenient to use the dimensions of [e-] for the atomic scattering factor. Its exact definition however is the ratio of the atom's scattering to the scattering for a free electron, and therefore it is strictly speaking a dimensionless factor or 'quantity of dimension one'. | A can of worms we do not want to open.... |
| 260,3,3 | cat ions should be cations | Thx Wolfgang! |
| 263,5,-2 | correlation should be relation | |
| 264,c6-14,-6 | Scattering should be The total Scattering | |
| 264,c6-14, end | Add: In practice, the straight-ahead scattering at 2θ = 0º cannot be separated from the unscattered direct (incoming or primary) beam. | Thx, Andy! |
| 265,s6-7,-5 | complied should be compiled | Thx, Andy! |
| 266, f6-14 |
needs to be replaced with new figure 6-14 Typesetter: new updated figure 6-14 (bmp) needs to be picked up from server - do not use old figure. |
gif here, new original on server after Sept 30th |
| 266,-1,-4 | space As should be space. As | Thx Wolfgang! |
| 269,C6-18,10 | The diffraction patterns should be In the first four rows, the diffraction patterns | |
| 273,c6-22,-5 | zone or should be zone (cusp) or | Thanks, AK! |
| 276,-3,-2 | zero, they are real should be zero, their structure factors are real | |
| 277,last line equation |
Square of sin misplaced, should be
 |
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| 278, 4th equation on page | closing parenthesis missing | download here. Thx, Wolfgang! |
| 280, E6-45 | xj should be Xj | download here. Thx, Wolfgang! |
| 281,Table 6-3 | The epsilon for general reflections should be 1 not zero | download corrected table here |
| 282, E6-47,6-48 | the four later capital greek psi are inconsistent in font with the body text and first 2 psi | Typesetter: use same letters with same font type as in body text download here. Thx, Wolfgang! |
| 283, E6-49 |
I think proportional is better than equal | download here |
| 285,F6-29 | Removed the stray 'plot area' at M-edges | updated figure 6-29 (gif) can be downloaded here. |
| 285,F6-29 | Typesetter: new updated figure 6-29 (bmp) needs to be picked up from server - do not use old figure. | |
| 287,2,-1 | Structure, or EXAFS spectrum. should be Structure (EXAFS) spectrum. | |
| 291,eqn6-60 | blue plus/minus signs need to be swapped | download here. Thx, Wolfgang! |
| 291,S6-2,Col2,3 | improved should be improve | |
| 294,3,-1 | no more than should be up to | |
| 297, B6-12,4 | resonance absorption should be absorption | |
| 297,B6-12,9 | Line break after pairs of reflection which should be pairs of reflections. | |
| 297,B6-12,9 | New paragraph Similarly, dispersive should be Dispersive | |
| 299,3,-3 | Ewald sphere should be resolution sphere | |
| 299,4,4 | delete by ignoring T | typesetter |
| 299,4,8 | after formulas, by ignoring the two operator should be by ignoring T the two operator | |
| 302,1,1 | the anomalous should be the imaginary anomalous | |
| 302,S6-13,col2,1 | le(a)vus should be l(a)evus | Thx, Wolfgang! |
| 306,1,-1 | delete last sentence They automatically....entire unit cell. | |
| 311, ref 30 | Methoda should be Methods | was ok in MS and copyedits |
| 320 |
I think a sidebar explaining the variance summations in bracket
notation should go there. Typesetter: Word doc in /data/book/chapter_7 on server | Available here |
| 321,C7-3,-4 | after ...in its range. Insert following sentence ...in its range (the FWHM is often used to describe functions that do not have a defined variance, such as the Cauchy-Lorentz function in spectroscopy). The percentage.... | |
| 324,4,-2 | bative should be native | |
| 327,last sentence | o_r should be over | |
| 329, E7-46 | The outer parentheses are too fat | typesetter |
| 329, E7-47 | The outer parentheses are too fat | typesetter |
| 330,2,2 | of calculated structure factor amplitudes should be of structure factor amplitudes calculated | |
| 332,6,2 | R-value should be R-value | |
| 335,1,2 | centuries and should be centuries, and | |
| 338,4,4 | and for our should be and from our | |
| 339,-2,2 | just as a should be just a | 9 lines up from bottom of page |
| 342,2,3 | x, y, z, B, n and for each should be x, y, z, B, n for each | |
| 344,3,-2 | thus intensities should be thus on intensities | |
| 348, last line | distribution of atoms along the should be distribution of atom contributions along the | |
| 349,4,1 | the variance of /greeksigmaetc/ our should be the variance /greeksigmaetc/ of our | |
| 349,6,1 (after E 7-98) | coordinates y should be coordinates imply | was correct in 2nd proof... |
| 350,C7-10,last | statistical analysis. should be statistical descriptors. | |
| 354, E7-116 |
P(Z) should be N(Z):
 | |
| 356,E7-118, E7-119 | The large parentheses are too fat | typesetter |
| 356,6,1 | Let is inspect should be Let us examine | |
| 357,C7-15,6 | regression though should be regression through | |
| 361,1,7 | imaginary parts should be imaginary axes | |
| 361,C7-18,7 | d \dot F should be d \dot f | |
| 362,3,2 | then needs should be needs | |
| 377,1,1 | the solution of should be the solutions of | |
| 378,3,4 | though a high should be through a high | |
| 378,5,-5 | the dispersive should be the anomalous and dispersive | |
| 380,1,1 | Huu at the University of California appears yellow highlighted | No highlight |
| 380, C8-7 | All my copies have a blue line/smudge in the caption | Production check |
| 383,S8-3,4 | 1960s and the should be 1960s. The | break sentence |
| 386, F8-13 | replace figure 8-13 with updated figure with different loop. Replace last sentence of C8-13 | New figure availabe here and in gallery |
| Typesetter: new updated figure 6-29 (bmp) needs to be picked up from server - do not use old figure. | Production check, update | |
| 386, C8-13 | Replace last sentence: ...mounting pin. The insert shows a harvested crystal in an older style nylon loop that is quite large for the crystal. Pre-fabricated loops are now availabe in many sizes, allowing to select a harvesting loop that matches crystal dimensions. The cross-hairs indicate the crystal location determined by image recognition software. Insert image courtesy of Andrea Schmidt, EMBL Hamburg. | Thanks for the new insert, Andrea! |
| 385,2,8 | with card or should be with a card or | |
| 386,2,4 | puck or a vial located in the puck (Figure 8-14). should be puck (Figure 8-14) or a vial located in the puck. | |
| 394,3,-4 | SHELXL and PHENIX/Refine should be SHELXL, REFMAC, and PHENIX/Refine | update |
| 395,3,7 | to abandon should be or to abandon | |
| 396,3,4 | latice should be lattice | |
| 400,1,-1 | only because should be because | |
| 403,2,-2 | of crystal should be of a crystal | |
| 406,4,-2 | sentence needs rewording should be | capable of handling incommensurate diffraction data and |
| 409,2,-5 | Wang should be B. C. Wang | |
| 413,4-2 | perferablycollected should be preferably collected | |
| 416,B8-10, -1 | Formula should be typeset like 8-24 | typesetter error - was correct in proofs |
| 418,1,5 | opposed should be related | |
| 419,2,-2 | which tends overall to result in worse should be which results in worse overall | |
| 419,3,9 | low penalty the should be low penalty. The | |
| 419,3,-4 | symmetry). should be symmetry. | |
| 422,T8-5; 423, T8-6 | Does the highlighting in the table have to look this ugly? | Revert to my original design. |
| 428,C8-42,3 | The probability distribution plot (CDF, left panel) should be The plot of the probability distribution function (CDF, left panel) | |
| 439, Figure | The figure is too small. | |
| 441,E9-7 | The equation is typeset larger than others. | Match typesetting |
| 442, e9-14 |
The equation is mistyped. it should be |
Hires jpg here Thx, Tobias! |
| On page 444 and 445 there are a series of correlated errors, resulting from the fact that I wrote 'convolution' several times when it should have been 'sampling'. The fact is that the diffraction pattern is of course the sampling (multiplication) of the molecular transform with the reciprocal lattice function, not convolution. This is correct in other places but I missed it here. |
Thanks, Erhard! |
|
| 444, F9-2 | convolution sign in lower panel should be multiplication symbol | updated figure 9-2 (gif) can be downloaded here. |
| 444,1,4 | convolution should be sampling (or multiplication) | |
| 444,C9-2,7 |
as a convolution of the reciprocal lattice with the reciprocal transform of the molecule. should be as a sampling (multiplication) of the molecular transform with the reciprocal lattice. | |
| 444,C9-2,-1 | delete corresponding | |
| 445,1,2 | Similarly, the sampling should be For their transforms, the sampling (or multiplication) | |
| 445,1,4 | to sampling should be to convoluting | |
| 445,B9-2,-3 | molecular envelope should be molecular scattering envelope | |
| 447,S9-2,6 | Friedels law should be Friedel's law | |
| 447,S9-2,col2,8 | or in practice compute should be or compute | update |
| 447,S9-2, end | Add: Some refinement programs such as REFMAC and SHELXL allow refinement against anomalous data. | update |
| 448,Paragraph 1 | Paragraph should be lead by Data truncation. | |
| 448,Paragraph 2 | Paragraph should be lead by Grid spacing. | |
| 449,C9-6,5 | occupation should be occupancy | |
| 450, E9-21 |
rho(r\sub\j) should be rho(r\sub\i) |
 |
| 451,C9-7,11 | hydrophobic Ile should be hydrophobic Val | .. |
| 452,1,3 | molecules is should be molecules from electron density alone is | |
| 454,C9-10,-7 | missing at should be missing, but at | |
| 455,1,2 | Figure 9-11 the should be Figure 9-11, the | |
| 455, C9-12 | last character should be a l (use a serif font) - looks like a backslash | |
| 457,1,1 | same effect should be same attenuating effect | |
| 457,1,2 | B-factors and should be B-factors, and | |
| 457,1,3 | B-factor should be B-factor, | |
| 459,3,3 | phase error should be mean phase error | |
| 461,C9-18,-3 | lower left should be lower right | |
| 462,S9-6,4 | or served should be or have served | I think so.. |
| 463,lastpara,2 | or finding should be or for finding | I think so.. |
| 467,last para, last line | Add sentence: Considering the centrosymmetry, the Patterson map has N(N-1)/2 unique peaks. | |
| 479,1,1 | FPA for each derivative should be FP for the native | |
| 479,B10-2,last sentence | replace with: As a result of the weaker signal, anomalous phasing requires slightly more marker atoms per residue, but even.... | |
| 481,1,1 | electronic should be scattering | |
| 481,2,-4 |
Update reference 21 the emerging PHENIX21 suite should be the PHENIX21 suite | 21. Adams PD, Afonine PV, Bunkoczi G, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica D66(2), 213-221. |
| 482,1,-5 | possible metal should be possible | |
| 484 last para,-3 | R-value should be RF-value | |
| 486 F10-11 | parentheses too fat | typesetter |
| 487,1,3 | 1-1, 2-2, 3-3, 1-2, 1-3, and 2-3 should be 1-2, 1-3, 2-3, 2-1, 3-1 and 3-2 | |
| 493,3,4 | heavy atom searches. should be more complex heavy atom searches. | |
| 500,S10-3,5 | described below. It was should be described in Section 10.7. CF was | |
| 502,3,1 | Sentence totally effed up - need to think | |
| 502,52 | anomalous contribution of an anomalous scatterer is should be anomalous scattering contribution f" is | .. |
| 504,S10-4,col1,10 | rapid should be fast | |
| 504,S10-4,col1,-2 | A version of SHELXE to be released soon119 will also include should be SHELXE now also includes......module.119 | update |
| 504,S10-4,col2,2 | will then provide should be provides | update |
| 507,2,-3 | phase angles should be phase angle distribution | |
| 507,T10-2,3 | replacement and should be replacement, and | |
| 511,1,5 | map: the should be map. The | |
| 511,1,-2 | amplitude should be amplitude: | |
| 519,6.line from bottom | addition of should be summation of | |
| 527,C10-26,10 | near-random phase should be near-random mean phase | |
| 530,3,-3 | resolution and we check should be resolution. We therefore check | |
| 535, 2,3 |
shelxc vta1 vta1_ fa –s0.5 –m20 –e1.0 –h -b should be shelxe vta1 vta1_ fa –s0.5 –m20 –e1.0 –h -b | correct in MS... |
| 535, 3,1 |
with the input to SHELXD should be with the input to SHELXC and SHELXD | |
| 535,last para, -3 | The returned model should be The model returned by the ARP/wARP server | |
| 537,2,-5 | f", and .... should be f". | delete rest of garbled sentence. |
| 538, C10-37, 9 | edge is also an should be edge is an | |
| 538,3,1 | of the MAD should be of our MAD | |
| 538,3,5 | structures and should be structures, and | |
| 547,1,4 | associated should be corresponding | |
| 547,4,2 | crystal structure. should be crystal structure, given only diffraction data. | |
| 550, t11-1, caption | better than average should be better-than-average | hyphens increase readability |
| 551,1,-6 | structur-ally | odd hyphenation |
| 551,1,-5 | pairs LV and HV and LC and HC are should be pairs LV and HV, and LC and HC, are | |
| 551,2,-2 | symmetry, any should be symmetry, and any | |
| 552, entire page | All RA,B and TA,B - also in equations - should be replaced with RAB and TAB for consistent notation | Figure 11-3 should be replaced, jpeg available here. |
| Note to typesetter: figure 11-3 has been updated - new fig (bmp) needs to be picked up from server - do not use old figure | ||
| 557,2,6 | crystal. Rotations should be crystal lattice. Crystallographic rotations | |
| 562,C11-8,6 | of reflections similar should be of reflections, similar | |
| 565,S11-2,last sentence | boundaries. should be boundaries, or in the case of domain swapping. | |
| 573,3,4 | difference should be experimental isomorphous or anomalous difference | |
| 576,2,3 | six parameters should be six placement parameters | |
| 578,S115,Col2,9 | largely sheet should be largely-sheet | |
| 578,S115,Col2,11 | largely helical should be largely-helical | |
| 578,1,7 | as a consequence many trials to find should be as a consequence, many trials are required to find | |
| 582,C11-24, -3 | crystallography symmetry should be crystallographic symmetry | |
| 584,3,4 | on a general position should be on a special position | |
| 586,4,4 | of oriented probe observed data. should be of the oriented probe and the observed data. | ... |
| 592,C11-27,4 | and not solvent should be (instead of solvent) | |
| 596,C11-26,-2 | Rice function and for centrics by the Woolfson function. should be Rice distribution and for centrics by the Woolfson distribution. | |
| 598,F11-30 | move figure and caption to top of page. | typesetter |
| 598,E11-58 | Brackets too fat, obscure superscript | typesetter |
| 603 |
Update reference 9 | 9. Adams PD, Afonine PV, Bunkoczi G, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica D66(2), 213-221. |
| 607,1,2 | model and local real space fitting of residues in electron density should be model into electron density and local real space fitting of residues | |
| 607,3,1 | errors remaining after rebuilding the model should be errors that remain after rebuilding, the model | |
| 613,5,-5 | 60% should be 60° | |
| 615,3,2 | data and is should be data. L is | |
| 622,1,2 | than model should be than adjustable model | |
| 622, B12-4, -6 | for errors should be for non-random errors | |
| 631, C 12-13 | Following a suggestion of George Sheldrick, add following paragraph after last sentence of figure caption: | Note that different programs may use different definitions and atom naming conventions in their chiral volume calcuation. SHELXL for example uses ASCII-alphabetic order of the atom names, and assigns positive chiral volumes for the L-amino acids. In the REFMAC/PHENIX monomer library the sign of the chiral volume is explicitly assigned for each atom, and with ligand order N CB C it is always negative for CA. If Cahn-Ingold-Prelog priority rules for absolute configuration (Sidebar 6-13) were strictly applied, cysteine would have R-configuration, all other chiral common amino acids would have S-configuration. |
| 634,5,4 | as restraint should be as a restraint | |
| 635,S12-5,col2,3,-1 | very computer intensive should be computationally intensive | |
| 635,S12-5,col2,4,4 | refinement. should be refinement against anomalous data. | |
| 636,1,4 | delete: the left panel of | |
| 637,2,1 | coordinates and should be coordinates, and | |
| 637,2,last 2 sentences | swap the last two sentences | |
| 640, 3,-3 | goodness-of-fit based should be goodness-of-fit | |
| 640,last line of body text | displacement vector should be displacement | |
| 643, end of C12-16 |
add following: Note
that in non-orthogonal crystal systems the always orthogonal truncation
ellipsoid axes do not correspond directly to reciprocal axes. From the
TRUNCATE manual: Direction 2 = b*;
direction 3 = perpendicular to
a* and b*; direction 1 = perpendicular to b* and direction 3. | Thx Matthias for that comment! |
| 644,2,4 | was deduced to should be was used to | |
| 647,3,-1 | delete: unnecessarily | |
| 650,line after e12-87 |
Hessian matrix is Nabla squared:
 | Correct in manuscript... |
| 650, above last line | p0-p1 should be p-p1 | needs to be checked |
| 653,S12-7,4 | diffraction and should be diffraction, and | |
| 657,1,3 | procedure should be program | |
| 657,1,4 | and is should be and it is | |
| 662, bullet3, -2 | necessary benefit should be necessary requirement or just necessity | Copyeditor to decide |
| 663, bullet5, 3 | not simply a should be not just a | |
| 667,3,5 | which snap should be which then snap | |
| 670 1,-1 | compensating for should be absorbing | |
| 670, C12-30, -5 | 2nls should be 1nls | Thx, Kay and Pete! |
| 672,2,1 | do have incorrectly should be do not have correctly | |
| 683,1,4 | 1/1000 should be 1/10000 | |
| 691 |
Update reference 133 |
133. Chen VB, Arendall WB, III, Headd JJ, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66(1), 12-21. |
| 695,3,-4 | R-factor should be R-value | that sucker slipped through.... |
| 701, T 13-2, lower header line | deviatiom should be deviation | Typesetter: table and figure were correct! |
| 707,2,first bullet,2 | effect of a well-built or incorrect ligand should be effect of either a well-built or an incorrectly built ligand | |
| 709,3,2 | known and should be known ligands and | |
| 711,S13-4,21 | density and should be density, and | |
| 711,C13-11,2 | low affinity should be low-affinity | |
| 711, F13-11 | relabelled low-affinity, drug-like | updated figure 13-11 (gif) can be downloaded here. |
| Typesetter: new updated figure 13-11 (bmp) needs to be picked up from server - do not use old figure. | ||
| 711, last paragraph | there is a blue smudge in my copies across the last 3 lines | typesetter |
| 719,S13-6,col2,1 | and B-correction should be and (negative) B-correction | |
| 729,1,2 | made) and should be made), and | |
| 733 |
Update reference 21 |
21. Chen VB, Arendall WB, III, Headd JJ, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica D66(1), 12-21. |
| 741 line after Eqn A-12 | its elements should be its diagonal elements | |
| 749,1,EQ A-54 | Formula is wrong - delete norm bars | .... thanks, Ian! |
| 749,C A-1 | Formula is wrong - delete norm bars |
 |
| 749, Paragraph below A-55 | follows what is considered should be follows the Euler Identity, considered | |
| 749, A-56 | Euler Identity has wrong sign... |
correct:
 |
| 750,3 lines below Eqn A-67 | \greekpsir should be \greekphir |
 |
| 754,Table A-6 | in Coulomb row, units are missing: | 1 C and 1 A·s |
| 788,middle of page margin | there are pink smudges in my copies | ?? |
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