Talk:X-ray crystallography/GA1

GA Review

Protonk comments

Images

• Image:Snowflake8.png. PD exemption for US government work is limited to employees undertaking their official duties. Rationale says that Bentley wasn't an employee. It is likely that copyright was never requested for the work and so it would now be in the PD anyway, but the tag needs to be checked and updated. Also the NOAA link is dead.

Fixed link to NOAA; added PD-1923 public domain tag to Commons image, since published in 1902 in U.S. Willow (talk) 20:54, 23 August 2008 (UTC)

• Image:X-ray crystals - slow evaporation 1 solvent.png et al. Tags are fine but I'm not sure what their function in the article is.

Removed with gallery. Willow (talk) 20:54, 23 August 2008 (UTC)

• Image:X ray diffraction.png For the size of this picture and its intended placement (the lead), I think the image is too busy. The image should be moved further down to a point where the reader will identify terms used within it immediately and be able to conceptualize the workflow visually. Perhaps something visually more simple, such as Image:Penicillin.png (with a larger XXX px argument than it has now) could be moved up to the lead to replace it.

I switched the images as you suggested, but used the zeolite image instead, since it suggests the periodicity of a crystal better than penicillin, don't you think? Willow (talk) 20:54, 23 August 2008 (UTC)

Sources

• WP:NOTES recommends shortening the citations if a bibliography is used. I read the bibliography in the current article (As it is not exhaustive) to be a "further reading" section in essence. Is this correct? If so I think that's great, but it should be renamed.

Yes, you're correct, and I renamed that section. Thanks! :) Willow (talk) 20:55, 23 August 2008 (UTC)

• Kepler, Steno, and follow-on works prior to 1900 are likely available in full text online. Should links to those sources be inserted into the footnotes (AFAIK, nothing requires it, but it might be nice for readers).

I'll look for those! Willow (talk) 19:13, 25 August 2008 (UTC)

I found an online copy of Kepler's work, which I added to the reference, but not of the others, unfortunately.  :( Willow (talk) 22:19, 25 August 2008 (UTC)

• Why do fn5 and fn8 have a "?" for the issue number?

I think that's the final page number? I wasn't sure what the final page was. Willow (talk) 19:13, 25 August 2008 (UTC)

• Footnotes 2,3,4,5, and 7 should indicate page numbers for the claim.

OK! Willow (talk) 19:13, 25 August 2008 (UTC)

• Bragg's citations are odd. Was it the intent of the authors to cite a claim in this fashion to 4 different sources? If so, the sentence should be changed to reflect that discussion occurred over more than 1907.

Yes, Bragg published his findings piecemeal; he took four articles to describe one crystal structure. Recall that, at the time, understanding what the data meant was hard, since the Bragg equation and other analysis methods hadn't been really developed. Willow (talk) 19:13, 25 August 2008 (UTC)

See the next point, I think. Protonk (talk) 19:18, 25 August 2008 (UTC)

• fn36, 37, 40, 41, 42, and 46 are all the same way. Given the claims in the article these footnotes are meant to source, I don't think that >1 reference is required. For instance, "The first application of X-ray crystallography to metallurgy likewsie occurred in the mid-1920s" cites 6 journal articles or conference reports, 2 of which were written in the 1930's.

These were generally meant to show a progression of the research, particularly if there was a series of structures published on a family of chemically related compounds, or a series of novel chemical bonds being discovered. Willow (talk) 19:13, 25 August 2008 (UTC)

I think that they are better footnoted as separate sources anchored to the same point in the text. Again, I may be wrong about this one but it allows individual links to each and also allows references that might eventually be cited elsewhere in the text to be linked as named refs without complication. Protonk (talk) 19:18, 25 August 2008 (UTC)

• A claim like "This was followed by several studies of long-chain fatty acids, which are an important component of biological membranes" seems like it should be verified by multiple sources, but I think the article would benefit from footnoting each OR (more preferably) citing a later review of the literature which makes that exact claim. See Wikipedia:Scientific citation guidelines.

OK, that makes sense to me. Willow (talk) 19:13, 25 August 2008 (UTC)

• Fn's 37, 49, 56 could be truncated to 3 authors et al.

If it's OK with you, I'd like to keep the authors written out, so that readers can recognize the name of the famous scientist(s) at the end of th elist, e.g., Wyckoff and Phillips at the end of reference 49. Willow (talk) 19:13, 25 August 2008 (UTC)

Fine by me. I'm unfamiliar with scientific citation guidance (as many papers are co-written by a half dozen individuals), so I can only suggest from my base of experience (APA, Chicago). Protonk (talk) 19:18, 25 August 2008 (UTC)

Style/MOS/Small points

• "X-ray crystallography is the science of determining..." Is it a science? A technique? The next sentence calls it a method.

"Method" is more accurate, so that's what I changed it to. Willow (talk) 17:57, 23 August 2008 (UTC)

• "...within a crystal from the manner in which a beam of X-rays is scattered from the electrons within the crystal" This wording is somewhat awkward.
• The lead makes no mention of the history or the Relationship to other scattering techniques, as WP:LEDE suggests.
• The lead moved into the topic material in a non-organic manner. the last paragraph in the lead should be moved to follow the first and the second and third paragraphs should be swapped. After that is done, take a look at the way the information would appear to a non-expert.
• "The key step in X-ray crystallography is the diffraction of X-rays from a crystalline material." "a" key step, maybe? Either way, this should not start off a paragraph.

I re-wrote the lead section. Is it better now? Willow (talk) 20:01, 25 August 2008 (UTC)

• "The oldest and most precise method of X-ray crystallography is single-crystal X-ray diffraction, in which a beam of X-rays are reflected from evenly spaced planes of a single crystal, producing a diffraction pattern of spots called reflections" this should be broken into two sentences.

I re-wrote this whole paragraph as well. Willow (talk) 20:01, 25 August 2008 (UTC)

• "...proposed several crystal structures in the 1880s that were ultimately proven correct by X-ray crystallography..." "experimentally validated"?

Excellent, I changed that. :) Willow (talk) 11:17, 24 August 2008 (UTC)

• "...spectral lines'" should wikilink to Spectral line

Great, also done. Willow (talk) 11:17, 24 August 2008 (UTC)

• "...Any remaining doubt was resolved in 1922, when Arthur Compton confirmed the photon model by studying the scattering of X-rays from electrons." the preceeding section here needs a rewrite to better contextualize the appearance of X-rays with the confusion and disagreement over the corpuscular and wave theory of light. As it stands the section is a tad confusing.
• $2d\sin \theta =n\lambda$ Renders small to me in tex, try forcing PNG?

I think I did the right thing, by adding a "\!" to the end, but it's hard for me to tell, since it always formats well for me. How does it look for you? Willow (talk) 11:17, 24 August 2008 (UTC)

• "As described in the mathematical derivation below..." an internal wikilink would be helpful here.

Added internal wikilink. Willow (talk) 11:17, 24 August 2008 (UTC)

• "...and non-covalent interactions" Is there a wikilink that can be helpful here?

Yes, I wiki-linked to noncovalent bonding. Willow (talk) 11:17, 24 August 2008 (UTC)

• "Also in the 1920s, Victor Moritz Goldschmidt and later Linus Pauling developed rules for eliminating chemically unlikely structures and for determining the relative sizes of atoms. These rules led to the structure of brookite (1928) and an understanding of the relative stability of the rutile, brookite and anatase forms of titanium oxide." What does "chemically unlikely structures" mean and what significance do these discoveries have for the article subject as a whole?

I need to explain this still. Basically, the idea is that early results from X. c. on simple structures clarified many rules of chemical bonding. Unfortunately, more complicated structures couldn't be solved, since they hadn't solved the phase problem yet. The X-ray data were consistent with several different arrangements of atoms. However, these scientists showed that many such structures could be removed from consideration because they were inconsistent with known facts from chemistry or from the early X. c. results. In lucky cases, such as rutile, all but one candidate structure could be removed from consideration. At least, that's how I understand it now. Willow (talk) 11:17, 24 August 2008 (UTC)

• "Compton scattering" should link to Compton scattering

Good catch — thanks, Proton! :) Willow (talk) 11:17, 24 August 2008 (UTC)

• "The Cambridge Structural Database contains over 400,000 structures; over 99% of these structures were determined by X-ray diffraction." Is there a source for that claim?
• "...crystallography to mineralogy began with the structure of garnet solved in 1924 by Menzer" Comma between garnet and solved? Or am I reading that wrong?

I wrote out that sentence more thoroughly. Willow (talk) 11:17, 24 August 2008 (UTC)

• "...an organic compound, hexamethylenetetramine, was solved..." is "solved" the wording used in the discipline to describe when a crystal structure is laid out through crystallography?

Yes, it is. I added that explanation slightly earlier, just after the earliest (table salt) structure. Willow (talk) 11:17, 24 August 2008 (UTC)

• "...approximate four-fold symmetry" What does this mean, precisely?

It means that a 90° rotation of the molecule in its plane would produce nearly the same molecule, but not exactly; if I recall correctly, there's an atom or two out of place. This was too much detail, though, so I removed it and focused on the relevant point that this molecule, aside from being an excellent dye, is very close in structure to very important biological molecules such as heme and chlorophyll. Willow (talk) 11:17, 24 August 2008 (UTC)

• "NMR spectroscopy" should be expanded in the first use, then abbreviated.
• "Therefore, X-rays are the "sweetspot" for wavelength when determining atomic-resolution structures from the scattering of electromagnetic radiation."Who uses the word sweetspot? Can we source this (I realize it appears to be a deduction from the drawbacks of lower or higher wavelength radiation but I'm sure some source can be found somewhere)
• "...which was used by Rosalind Franklin in determining the double-helix structure of DNA" I'm surprised this hasn't resulted in some consternation. I'm glad this article points to her. :)

Me too. :) The statement is correct, though. Watson and Crick hypothesized a structure, one that happens to be correct for B-form of DNA but incorrect for the A-form and Z-form; an earlier hypothetical structure of theirs happened to be incorrect. The structure was determined only by the experimental fiber-diffraction data of Rosalind Franklin and, much later, single-crystal structures. Willow (talk) 19:04, 21 August 2008 (UTC)

Oh absolutely. I just expected that it would be fairly common for wandering editors to drop by and say something along the lines of "ZOMG! Watson and Crick did this, not her". Protonk (talk) 19:39, 21 August 2008 (UTC)

• "However, it is not as well-suited as monochromatic scattering for determining the full atomic structure of a crystal. It is better suited to crystals with relatively simple atomic arrangements, such as minerals." This probably needs to be cited.
• "Small molecules generally have few degrees of conformational freedom" wikilink to Degrees of freedom (physics and chemistry), or is that too abstract? either way, this needs some slight explanation.
• "collimated" is there a wikilink that can go here?

Linked to collimator, which was better than collimated light. Willow (talk) 11:17, 24 August 2008 (UTC)

• "(The explanation for the relevance of this technique is given below.)" Should link to the transform section

Added internal wikilink — thanks again for catching that! :) Willow (talk) 11:17, 24 August 2008 (UTC)

• "As a rule of thumb, Rfree should be approximately the resolution in Ångströms divided by 10" this should be sourced.
• "Many structures obtained in private commercial ventures to crystallize medicinally relevant proteins, are not deposited in public crystallographic databases." As pedestrian as this seems, this could benefit from a source or even a link to articles we have on some private databases.
• $f(\mathbf {r} )=\int {\frac {d\mathbf {q} }{\left(2\pi \right)^{3}}}F(\mathbf {q} )e^{i\mathbf {q} \cdot \mathbf {r} }$ q is defined below, would it help to define r?

D'oh! ;) Now it's defined. Willow (talk) 11:17, 24 August 2008 (UTC)

• "The electron density f(r) is a real function, which imposes a constraint on its Fourier transform" Link to Function of a real variable and perhaps explain why the constraint exists (if it can be done so pithily)

Short explanation given, but I could explain this more with a formula; would it be worth it? Willow (talk) 11:17, 24 August 2008 (UTC)

Perhaps. I think the Function of a real variable is a better target than real number. Should I merge that with Real number and point the target to a subsection? Protonk (talk) 14:29, 25 August 2008 (UTC)

I'm sorry, I'm not sure if I understand> I think that most readers will accept that the position vector r is real not complex, so I'm not sure what the link to Function of a real variable will bring us? The problem is really whether f is a real function of a real variable or a complex function of a real variable. To guarantee that f is a real function of a real variable, a constraint on its Fourier transform F(q) must be satisfied. How about this solution? I'll write out the constraint and if you think it's too long-winded, we can get rid of it again. Thanks you! :) Willow (talk) 16:21, 25 August 2008 (UTC)

This is probably coming from my lack of understanding more than anything else. I'll take another look and see if I can get it right. Protonk (talk) 18:14, 25 August 2008 (UTC)

• "...the curvature of the Ewald sphere (add Figure to illustrate this)" Hmm.  :) Perhaps Image:Ewald.gif? either way this section should be expanded to better explain what the construct means or removed (As it isn't really necessary within the article).
• "In principle, this could be used to determine the crystal structure directly; however, it is difficult to realize in practice..." source?

Layout

• Advantages of a crystal: the contents of this section fit much more neatly in with Diffraction theory than their current location.

Yes, that's a great idea. I put it at the very end, which rounds out the article nicely. :) Willow (talk) 17:56, 23 August 2008 (UTC)

• Overview of single-crystal X-ray diffraction section: should this be a subsection in the methods portion of the article? I think it works better to start with history as the section now reads like a quick intro and is forgotten by the time we move to the history section.

I also moved this section as you suggest. This Overview was just the relic of a longer lead that I wrote, but which another editor objected to. Willow (talk) 17:56, 23 August 2008 (UTC)

• "In some cases, the crystallographer can identify good solution conditions for growing very small crystals that do not continue to grow and which are too small for crystallography. In such cases, the tiny crystals can be transferred to new solution conditions that favor growth more strongly; the small crystals act as pre-nucleated seeds for subsequent growth. In an alternative approach, a larger but poor-quality crystal may be crushed, and the pieces used as seed crystals to obtain higher quality crystals." I think the section would be better with this paragraph removed.

It is a rather technical point. I'll remove it as you suggest. Willow (talk) 17:44, 23 August 2008 (UTC)

• What function does the Gallery section serve?

I didn't add that. It illustrates some of the many ways of getting a molecule to crystallize. I think the images would be better incorporated into the main text of a daughter article on crystallization methods, so I moved the gallery to here for now. Willow (talk) 17:44, 23 August 2008 (UTC)

• WP:EL says the list of external links should go at the end.

Now that the gallery has been moved, they do. :) Willow (talk) 17:44, 23 August 2008 (UTC)

Overall

Ok. Overall a very informative article. It is clear that an effort was made to make a relatively complex process available to the general reader. I'm placing this article on hold pending a resolution of the issues with the lead, layout, sources and some of the minor quibbles above. Thanks for the opportunity to review such a fascinating subject. As always, my errors in understanding and mathematics are my own. Protonk (talk) 18:02, 21 August 2008 (UTC)

• Passing this article. I still have questions as to how the sources are arranged for specific claims but that isn't something for GAN given how improved the rest of the article is from the point of nomination. Protonk (talk) 17:36, 26 August 2008 (UTC)

Thank you so much, Protonk! I'm going to go to sleep very happy and have good dreams tonight. :) I'll try to satisfy all of your remaining concerns—I see some other problems as well—but I'm also really grateful for the time you've put into reviewing and improving these articles. You're a gem! :) Willow (talk) 03:36, 27 August 2008 (UTC)