Talk:X-ray crystallography

From Wikipedia, the free encyclopedia

WikiProject Physics This article is within the scope of WikiProject Physics, which collaborates on articles related to physics.
B This article has been rated as B-Class on the assessment scale.
Mid This article is on a subject of Mid importance within physics.

Help with this template

Comments:
Molecular and Cellular Biology WikiProject
MCB Portal
This article is within the scope of the Molecular and Cellular Biology WikiProject. To participate, visit the WikiProject for more information. The WikiProject's current monthly collaboration is focused on improving Restriction enzyme.
B This article has been rated as B-Class on the assessment scale.
High This article is on a subject of High-importance within molecular and cellular biology.

Article Grading: The following comments were left by the quality and importance raters: (edit · history · refresh · how to use this template)

The single crystal diffraction section needs a discussion of inorganic materials (e.g. that XRD is used extensively in silicon and compound semiconductor work).
To-do list for X-ray crystallography: edit · history · watch · refresh

Here are some tasks you can do:


    • Define and resolve the "factual dispute"
    • Eliminate the "unbalanced" tag
    • Fuller treatment of mineralogical and metallurgical applications
    • Add more about small-molecule work and other fields
    • Add more inline references instead of relying on the bibliography
    • Make lots of good diagrams (see Talk page for lists)
    Priority 1 (top) 

    Contents

    [edit] Early message?

    Dear Chemgrrl et al:

    When use XRD to characterize CNTs, is the "d" in Braggy Eqn. the diameters of CNTs?--Lin

    [edit] um.. I'm doin a science essay on xray crystallography

    Can you answer these questions for me???

    • What is it?
    • What is it used for? and..
    • What minerals are used?

    thank you for your time

    gracee***

    The article itself should answer the first two questions. As far as what minerals are used, I'm not sure I understand the question.

    None of my business really, but looks neutral to me. 12.14.174.162 04:52, 25 June 2007 (UTC)

    If you're asking what minerals this type of diffraction can be used on, the answer is "basically anything". It won't work very well on obsidian, because amorphous solids don't diffract very strongly.
    As far as testing the instrument itself, the only thing I've seen used is lithium fluoride, but I think graphite is also a fairly practical material to produce controlled diffraction. Honestly, though, you can use anything with a known crystalline structure, it's just that more complicated structures make the math more difficult.
    As far as the minerals used to make one, a fair amount of iron and copper ore go into making the machine in general, and you need some tungsten for the X-ray tube's filament. Some parts are stainless, so that takes chromium and nickel, and there are usually some parts made of glass and some control circuitry made of silicon. Some petrolium goes into making insulators for the wiring and such, and a fair amount of fossil fuels are quite likely to be burnt at the local power station in order to run the thing.
    Could you ask a more specific question?--Joel

    You can determine the 3d structure of -pretty much- any molecule using x-ray crystallography. Could be small molecule or really huge molecules like proteins. All you need is crystals of that molecule really. -Ert

    [edit] Methods

    It would be helpful if there was a section on methods for determining structure (eg. Laue methods, Debye-Sherra method, etc.). I'm just researching it so I don't think I'd be much help atm.

    Laue method is mentioned, as well as Debye-Waller. What is the Debye-Sherra method? Thanks. LostLucidity (talk) 16:17, 5 April 2008 (UTC)
    Debye-Scherrer, I expect. - Eldereft ~(s)talk~ 17:33, 5 April 2008 (UTC)
    Okay, thanks. It's not mentioned in the article though. LostLucidity (talk) 17:45, 5 April 2008 (UTC)

    [edit] Proposed reorganization

    Hi everyone. I am considering doing a fairly major edit of this page. I do this (biological crystallography) for a living and am more than happy to spend some time putting more about it in the public domain. This is fairly complicated area, and I am happy to take any and all suggestions about it. I think there is a fair argument for giving Biological Crystallography its own page, but for now I'll do the edit in page. I was thinking about doing stuff under the following sub-headings

    • Diffraction Theory
    • Crystallisation
    • Data Collection
    • Phasing
      • Molecular Replacement
      • Heavy Atom Phasing
    • Structure Refinement

    Let me know what you think... Bassophile 20:55, 9 February 2006 (UTC)

    Hi Bassophile,
    I also did X-ray crystallography for a living (still do sometimes). I worked at the Weizmann Institute of Science and contributed to set up it Structural Proteomics Center. I would be wiling to assist you in expanding the X-ray crystallography page, especially the biological crystallography (and crystallization) sub-points.
    All the best, TheSpirit 13:58, 14 February 2006 (UTC)

    Hi The Spirit. I'd appreciate any assitance/comments/criticism you have... I think it's a little patchy at the moment. I'm trying NOT to include too much nasty theory, but I suppose some is inevitable. I'm also trying not to duplicate what has already been done elsewhere. There is a nice section on unit cell which includes a good introduction to symmetry etc, which is why I've left that out. I've also not gone into Bragg's and Laue's laws/conditions as they too are covered elsewhere. Let me know what you think so far.

    Cheers, Bassophile 15:30, 14 February 2006 (UTC)

    [edit] Plea for discussion of major changes

    A little discussion about your rather major changes to this page would be appreciated! I would argue that the crystallisation and data processing of small molecules and the crystallisation and data processing of macromolecules, whilst being superficially similar, are sufficently different to merit their separate sections, as I had originally laid out. I suggest we combine our efforts and deliniate Small molecule and macromolecular crystallography whilst highlighting the differences and similarities between the two disciplines... Bassophile 20:20, 28 March 2006 (UTC)

    [edit] Merger with Crystallography article

    I removed the notice about merging this article with crystallography. That article clearly discusses other techniques beside x-ray. It is not clear to me that they need to be merged. Rmhermen 21:01, Nov 14, 2003 (UTC)

    Yes, crystallography addresses additional techniques, but those others are also based on diffraction from crystals and on the construction an image by fourier transformation, and so a lot of the explaining that needs doing for one of them needs doing for all of them. I think we should have one good explanation of the commonalities in one article and links to specific articles just for the fine points, such as that a lot of X-ray stuff is going on at synchrotrons and figures in big international proteomics initiatives. 168... 21:51, 14 Nov 2003 (UTC)

    Not the same as merging though. I don't know that there is anything wrong with having a detailed explanation of all techniques at crystallography, and a brief explanation and fine points at each kind. Some general description needs to stay here for people who arrive directly by links to x-ray crystallography. It just isn't polite to click on a link and be immediately told to click another to get the basics and then come back. Rmhermen 14:07, Nov 15, 2003 (UTC)

    [edit] Temperature

    The article states that usually one works at 100K. Has it always been this way (and if so, why)? I'm reading an Acta Cryst. of 1976 and it doesn't mention the work temperature. It wold be very interesting to me to know whether I should assume that the determination was done at room temperature or at 100K... Thanks :-)

    No, rt was common until cryojets were developed in the 1990's. The use of low temperature significantly improves the data due to less molecular motion and disorder.Hokietiki@hotmail.com 22:38, 29 January 2007 (UTC)

    [edit] Resolution

    I updated the link to resolution to Sensor resolution. This might have needed to be a link to Optical resolution. Feel free to change it if you have more insight in to this then me. --STHayden 22:21, 6 August 2006 (UTC)

    [edit] Separate page for macromolecular crystallography?

    I think protein crystallography should have its own page (possibly redirected to from 'macromolecular crystallography') -- different refinement approaches, different ways of phasing, much more trouble with crystal growth ... Fivemack 15:55 21 September 2006

    It has its own subheading in the article but I think its too short to be stand alone. LostLucidity (talk) 16:47, 8 April 2008 (UTC)

    [edit] UserBox

    Would anyone like this:

    This User is an X-ray crystallographer

    Bassophile 13:46, 11 January 2007 (UTC)

    [edit] Article is incoherent

    It's not clear whether the article is about x-ray crystallography (generic field of study and family of analytical techniques) or about the analytical technique of single-crystal x-ray diffraction. It also seems that other methods such as powder diffraction are mixed up in this article. In my line of work few people would refer to powder or thin-film diffraction as "crystallography", whereas the single-crystal jocks call themselves "crystallographers". I have substantial experience in non-single-crystal methods and have started an alternative page x-ray diffraction to clear this up. Irene Ringworm 16:43, 28 February 2007 (UTC)

    I agree. This page is trying to be too many things at once. Maybe splitting powder diffraction methods and single crystal methods up is the right thing to do. If we stick a disclaimer at the top, refering people interested in power diffraction methods to your page - would that be clearer??? Bassophile 09:23, 1 March 2007 (UTC)
    One vote for Basophile. Plese split the diffraction and single crystal methods up. It would give the article much more focus. 130.216.191.182
    I don't think an explicit disclaimer is necessary. I've cleaned up the introduction to explicitly state the scope of the article and think that should suffice. Also, my x-ray diffraction page explicitly refers people to the crystallography page in the opening section. Irene Ringworm 14:50, 1 March 2007 (UTC)
    Excellent. I think that this looks much less incoherent. Not just for some time to do some more editing... Bassophile 13:05, 5 March 2007 (UTC)

    [edit] Lead picture

    I would call the ribbon structure in the lead image a molecular model rather than an atomic model. Agree? ike9898 21:41, 8 May 2007 (UTC)

    Sure, or how about just "ribbon diagram"? Willow 22:19, 8 May 2007 (UTC)
    In any case, it's in the wrong place in the sequence. First you find an approximate set of phases, then you figure out where the nuclei are, only then do you produce anything that ressembles the electron density diagram. Don't forget that most X-rays are diffracted by the core electrons, not the valence electrons. Physchim62 (talk) 06:48, 9 May 2007 (UTC)
    Hi Physchim62! :) Forgive me, but the order is correct as is, I believe. The phases are used to invert the Fourier transform of the electron density, which includes both the core and valence electrons, no? After contouring the resulting real-space electron density at an appropriate level, the nuclei are positioned within that density; the nuclear positions are then used to obtain the calculated amplitudes Fc. For very high resolution structures (<1 Å), the contoured electron density often appears as small blobs (maybe 0.5 Å across) centered on the nuclear positions; but you or the computer still have to place the nuclei within the density after that real-space electron density is calculated from the phases. At least that's my understanding; perhaps you've done differently? Willow 11:21, 9 May 2007 (UTC)
    Not really. The phase problem is initially solved by finding the locations of the heavy (or anonymously scattering atoms). When the fourier transform is run using this first draft phases, seeveral areas of "negative" electron density show up which are either atomic nuclei (in a small-molecule structure) or structural features in a macromolecule. An α-helix, for example, will show up as a tube of negative electron density at this point. The crystallographer than places appropriate atoms or structures where there is significant electron density, recalculates the phases and reruns the fourier transform. The the process is repeated until as many nuclear positions as possible are known. Note that in calculating the phases, the crystallographer almost always uses tabulated values for atomic electron densities: it is rare to have a structure determination in which there is sufficient data to calculate the electron density distribution for an individual molecule based only on diffraction data. Physchim62 (talk) 12:53, 11 May 2007 (UTC)
    So this discussion is trying to determine if the ribbon diagram should precede the electron density map, in the sequence of steps shown in the picture? User:Physchim62, are you satisfied if the order is reversed, or are you proposing a wider change? EdJohnston 19:45, 11 May 2007 (UTC)

    [edit] Recommendations for improvement (minimal requirements for FA)

    The following suggestions were generated by a semi-automatic javascript program, and might not be applicable for the article in question.

    • Consider adding more links to the article; per Wikipedia:Manual of Style (links) and Wikipedia:Build the web, create links to relevant articles.[?]
    • There may be an applicable infobox for this article. For example, see Template:Infobox Biography, Template:Infobox School, or Template:Infobox City.[?] (Note that there might not be an applicable infobox; remember that these suggestions are not generated manually)
    • Per Wikipedia:Manual of Style (numbers), there should be a non-breaking space - &nbsp; between a number and the unit of measurement. For example, instead of 3 mm, use 3 mm, which when you are editing the page, should look like: 3&nbsp;mm.[?]
    • Per Wikipedia:Manual of Style (numbers), when doing conversions, please use standard abbreviations: for example, miles -> mi, kilometers squared -> km2, and pounds -> lb.[?]
    • Per Wikipedia:Manual of Style (numbers), please spell out source units of measurements in text; for example, the Moon is 380,000 kilometres (240,000 mi) from Earth.[?] Specifically, an example is 0.1 nm.
    • Per Wikipedia:Context and Wikipedia:Build the web, years with full dates should be linked; for example, link January 15, 2006.[?]
    • Per Wikipedia:Manual of Style (headings), headings generally do not start with articles ('the', 'a(n)'). For example, if there was a section called ==The Biography==, it should be changed to ==Biography==.[?]
    • Per WP:WIAFA, this article's table of contents (ToC) may be too long- consider shrinking it down by merging short sections or using a proper system of daughter pages as per Wikipedia:Summary style.[?]
    • This article may need to undergo summary style, where a series of appropriate subpages are used. For example, if the article is United States, than an appropriate subpage would be History of the United States, such that a summary of the subpage exists on the mother article, while the subpage goes into more detail.[?]
    • There are a few occurrences of weasel words in this article- please observe WP:AWT. Certain phrases should specify exactly who supports, considers, believes, etc., such a view.
      • it has been
      • might be weasel words, and should be provided with proper citations (if they already do, or are not weasel terms, please strike this comment).[?]
    • Please make the spelling of English words consistent with either American or British spelling, depending upon the subject of the article. Examples include: meter (A) (British: metre), fiber (A) (British: fibre), recognize (A) (British: recognise), realize (A) (British: realise), ization (A) (British: isation), isation (B) (American: ization), analyze (A) (British: analyse), analyse (B) (American: analyze), modelling (B) (American: modeling).
    • Watch for redundancies that make the article too wordy instead of being crisp and concise. (You may wish to try Tony1's redundancy exercises.)
      • Vague terms of size often are unnecessary and redundant - “some”, “a variety/number/majority of”, “several”, “a few”, “many”, “any”, and “all”. For example, “All pigs are pink, so we thought of a number of ways to turn them green.”
    • Please ensure that the article has gone through a thorough copyediting so that it exemplifies some of Wikipedia's best work. See also User:Tony1/How to satisfy Criterion 1a.[?]

    You may wish to browse through User:AndyZ/Suggestions for further ideas. Thanks, Wim van Dorst (Talk) 22:01, 9 May 2007 (UTC)

    [edit] Reference please

    Can someone provide a reference for "Twinning often occurs when the unit cell has a net electric dipole moment (ferroelectric crystals), because of a subtle interaction between the dipoles of the bulk crystal with polarization charges expressed on the crystal's surface."

    Bassophile 07:43, 22 May 2007 (UTC)

    You're quite right, I should do that. I've been rather lame about providing references for most of what I wrote, but I'll try to tackle that this week. Hoping that you liked the rest of the text, Willow 21:59, 22 May 2007 (UTC)
    It's all good at the moment - when I get some spare time I'll do some more work myself, Bassophile 07:34, 24 May 2007 (UTC)

    [edit] Pictures. We need pictures.

    Hi all!

    The article would benefit from a lot more pictures, don't you think? I'll try to make schematics for the sitting/hanging drop methods and for the kappa goniometer, but my drawing skills are lame and it would be better to have real photographs. A photograph of a precipitate droplet might be nice, too. Images of the electron density at various stages of the phase refinement would also be great, perhaps as a mesh surrounding the final structure as a stick model? Any help would be much appreciated, Willow 14:45, 24 May 2007 (UTC)

    No worries - I put in the Electron density picture and I have loads more where that came from - I can also provide hanging drop schematics. Bassophile 14:50, 30 May 2007 (UTC)

    [edit] Ever used by geologists/crystallographers/mineralogists? I think so.

    This article implies that this technique is solely used for determining the structure of organic molecules and inorganic compounds. However, x-ray crystallography is the science of using x-ray diffraction to understand the structure of crytalline materials, not of molecules per se, and as such includes its use as a tool for geologists looking at the crystal structure of minerals. Is there some reason I am missing that this article has declared the technique to only be a tool in the life sciences? KP Botany 18:44, 27 May 2007 (UTC)

    There has been some discussion of this in the past. Most small molecule crystallography seems to have be placed in powder diffraction (yes, I am aware there is a difference!). If you wish to add a section pointing out the differences between small molecule and macromolecular crystallography, such as more emphasis on direct methods, different crystallisation methods etc... go for it (be bold)! Bassophile 14:55, 30 May 2007 (UTC)

    Whether or not I include anything, the article can't be written as if it is something that is not, ie, the entirety of x-ray crystallography, when it is not actually about x-ray crystallography, but only part of it. It's like writing an article about radio waves and labeling it the electromagnetic spectrum. I will tag it for now. KP Botany 17:20, 30 May 2007 (UTC)

    I think the inorganic chemistry aspects of X-ray crystallography seem a bit underrepresented too. X-ray crystallography provides one of the strongest evidence for the postulated structure of a complex, while the life sciences aspect seem to be overly emphasized. In particular, I refer to the diagrams and pictures, and the "Methods" section. --Rifleman 82 17:38, 30 May 2007 (UTC)
    I do agree that the inorganic side is under represented, and that as it stands the article does not give a complete view of crystallography However, as that is not my speciality, I do not feel particularly qualified to write it . If you feel you are so qualified, then please, go ahead and edit it. To simply tag it and move on without contributing strikes me as a little bit of a cop out. Either we split small molecule and macromolecule crystallography into two different sections/pages, or we edit this page to include/highlight any differences. Your input would be greatly appreciated. Bassophile 12:57, 31 May 2007 (UTC)
    All I have is a brief understanding of Bragg's law and Laue. Otherwise, I'm not qualified to comment either. However, I am a user of the product generated from single crystal X-ray crystallography, so I can understand its importance in inorganic chemistry. That said, I didn't tag the article. --Rifleman 82 15:02, 31 May 2007 (UTC)

    Bassophile, while I'm happy you're so knowledgable on the subject that you can write on the fly, I can't. My concern is that readers coming to the article as it now stands will think that x-ray crystallography is a technique for studying organic molecules. It isn't, it is the science of looking at the structure of crystals, some of which are organic, to learn their atomic and/or molecular arrangements. As long as there are sentences like this in the article, "X-ray crystallography is used in chemistry and biochemistry to determine the structures of inorganic compounds, DNA, RNA and proteins," which are clearly false, it has to be tagged to warn readers. Although I've done some x-ray crystallography, it has been quite some time, and I am unwilling to write on the fly about something so complex that I haven't done in a while. When I get my facts straight I will add to this article. You might consider renaming this x-ray crystallography (biological) in the meantime, if you simply don't know anything about the materials aspect, or don't have the inclination to add anything about it. KP Botany 18:15, 31 May 2007 (UTC)

    Hi all, the article at present is a work in progress, and I'll be happy to add the material science angle once I return. Unfortunately, I'm traveling to my sister's graduation and won't be back until the 2nd week in June. I can try to add dribs and drabs before then, but it'll be difficult; can you all be patient? If you could outline specific topics you would like to see added, that would be great. I'll drop in as I can, Willow 12:09, 1 June 2007 (UTC)
    PS. If you review the article carefully, you'll see that most sections pertain to all forms of X-ray crystallography (hence, there's no need for a split), which I've taken to be synonymous with single-crystal X-ray crystallography. Do people feel that we need to include a section about poly-crystalline methods such as powder diffraction? Personally, I would favor not including such a section, but I can draft a blurb if the consensus is to include one. Willow 12:13, 1 June 2007 (UTC)
    PPS. The History section really needs work; anyone want to tackle that? Thanks! Willow 12:24, 1 June 2007 (UTC)

    Willow, the real problem now is the article is entirely geared towards biological. I see the introductory paragraph has been changed, but from there it boldly goes on as if the article is all about the biological. I think making it accurate is more important than hurrying up, and, imo, the best Wikipedia editors are those who have lives outside of Wikipedia, so please enjoy your time with family then add material as appropriate. I know people don't like tags like this, but it is important to alert readers that there are issues with article, so they know to be careful about what they take from the article. I think the article should be general about x-ray crystallography, as that is its title, and other articles should deal with the specific techniques. See Electron microscope and Transmission electron microscope and Scanning electron microscope for a good idea of how it can be done. It would be wonderful to get a good series of articles on Wikipedia for the layman on these topics. KP Botany 18:53, 1 June 2007 (UTC)

    I think that to split the page into Biological and otherwise has advantages and disadvantages. My personal feeling is that whilst adding the inorganic stuff in would make it a more complete & authoritative article, it may make it too long (there are upper limits, are there not?). Does anyone out there agree/disagree? Bassophile 07:53, 5 June 2007 (UTC)
    Hi all, thanks for being patient with me! :) I'll be back home about a week fom now, but I'll try to drop by as I can. I have to say that I don't see the article as biology-centric. At least sections 1 and 3-5 are general to all crystallography, although perhaps I haven't done non-molecular crystals such as metals full justice. But perhaps there are too many biological examples used for illustration? Section 2 — the infamous History section — is indeed pretty bio-centric and could be drastically improved; however, it's also true that difficult crystal structures such as proteins have helped the field advance as a whole, no? I really don't think we need to split or change the article much to cover non-bio crystals, just add a sentence or two here and there, and maybe re-phrase things to include non-molecular crystals. Do others agree with that? Willow 11:17, 5 June 2007 (UTC)
    No, I don't agree with you. The opening sentence is, "X-ray crystallography, which includes the technique of single-crystal X-ray diffraction, is the oldest and most common crystallographic method for determining the structure of molecules." Actually X-ray crystallography is used to determine the structure of crystals, in mineralogy this includes looking at the ordering of atoms and molecules within a crystal. Then, the opening paragraph closes with this sentence, "Such crystal structures have many scientific and medical applications; for example, they can shed light on the molecular events of enzyme catalysis or serve as the basis of structure-based drug design." Again, the entire emphasis is on the biological. The steps are for producing biological molecules for crystallography, and the closing paragraph of the lead section differentiates based upon biological terms and techniques, "generally discerns small-molecule crystallography, which typically involves molecules with fewer than 100 atoms, from macromolecular crystallography, which can involve tens of thousands of atoms." Biological, biological, biological. If you don't have time to add the materials or geological, that's fine, and if you don't have the background, that' fine, but please don't continue saying it is not biased when it starts out so clearly as an article on biological x-ray crystallography. KP Botany 20:43, 10 June 2007 (UTC)

    (reset indent) I've gone over the article again. Please bear with me, if I appear biased. I can only speak for my own experiences. I have absolutely no experience with protein crystallography, and I have no knowledge of the history of crystallography beyond Bragg's law. My experience is as an inorganic chemist - the use of X-ray crystallography to determine the connectivity and the solid state conformations of organometallic compounds.

    These are my suggestions.

    1. Reduce the number of biomolecule pictures, and introduce some of inorganic compounds and crystal structures. The pictures are currently exclusively that of biomolecules, and that may give the reader the wrong impression that protein crystallography is what x-ray crystallography is all about.
    2. "History" can include some history of inorganic crystals.
    3. (already done) Move protein-specific information to the rear of "Crystallization", after the general information.
    4. The use of crystallization aids like triphenylphosphine oxide has been described (see that article). I believe that some people use derivatives, different counteranions, etc. to infer the connectivity of the original compound which doesn't crystallize well. I am aware of such techniques but I am not confident of describing them. Perhaps someone who is can do so.

    With regard to #1 and #2, I'll try my best and find some information. Perhaps someone can help with #4. --Rifleman 82 14:09, 5 June 2007 (UTC)

    If there is a lot more information on protein crystallography, perhaps it should be split into a separate article "protein crystallography", which discusses the finer points. The broad strokes can remain here. I.e. diffraction theory, sample prep, data collection and analysis. --Rifleman 82 14:16, 5 June 2007 (UTC)

    Some good starting suggestions have been offered by Rifleman. KP Botany 20:43, 10 June 2007 (UTC)
    Thanks for your ideas and good work, Rifleman 82! :) I worked on the lead slightly; does it read better now? I'll try to add other elements over the next few days.
    I do appreciate that we need to spend more time covering crystals that are not molecular, such as metals and salts. However, unless I'm misunderstanding something, "molecular crystal" does not necessarily mean "biological molecular crystal". For example, a crystal of anthracene — which is found in no living organism, to my knowledge — would be a good example of "small-molecule crystallography", right? Similarly, one could imagine an inorganic polymer that might make a "macromolecular crystal", no?
    Hoping that we're moving in the right direction, Willow 21:29, 12 June 2007 (UTC)
    How about just getting something in on crystals? Minerals? Rocks? While it may seem far-fetched, x-ray crystallography is done to identify the crystal structure of crystals--to learn the arrangement of the molecules and atoms that make up a crystal, as in rock-forming mineral. I can probably get some images, but I haven't done any in years, and it would take more than a casual read to get up to snuff on it. Can we just include its geological application? KP Botany 05:30, 13 June 2007 (UTC)
    So the page now seems much more "all encompassing" now - I must commend those who have done all the work - can we remove the tag yet?

    130.88.210.108 14:09, 3 July 2007 (UTC)

    Thank you for your kind words! I haven't had the chance to fulfil KP's request for more mineralogy, though. I'll dash off something quickly now, with the promise of better things to follow. If we're agreed and if we believe one another to be sincere in our wish to improve the article, it might be nice to remove the tag. Thanks again, Willow 15:57, 3 July 2007 (UTC)
    Let me read the entire article. The introductory paragraph needs a tweek to two but is generally excellent--FA material. KP Botany 18:12, 4 July 2007 (UTC)

    It still looks very unbalanced as there is a lack of pictures, references and external links for non-biological applications. Even the history section is dominated by biological developments, leaving a couple of short sentences for the early history. GB 03:25, 5 July 2007 (UTC)

    Thanks for looking, GB. I think the tag should stay while this is an issue, so that the general reader does not mistake this for a complete article on the topic. KP Botany 03:29, 5 July 2007 (UTC)
    Yes, I'm keenly conscious of the sketchy state of the History section, as I wrote above. The lack of references is also a failing that will have to be amended before going to FAC, although many of them may be drawn from the bibliography; I just need time to craft the proper inline citations. I'll try and work up a few pictures; I have some nice ideas for the Ewald sphere, although my imagination may exceed my powers of realizing it. ;) If you have specific suggestions for pictures or other helpful additions, please let me know; they would be most welcome. Thank you for your insights, Willow 10:45, 5 July 2007 (UTC)

    [edit] Article assessment as of July 2007

    Hey there small molecule lovers! I have re jigged the phasing & history section to pay a little more homage to the elucidation of small mols - I even made and dropped in a picture of Penicillin for your enjoyment and delight - I am content and happy to do some more tweakage in most sections, but I am afraid I am not au fait with small molecule crystallisation (drop in it something volatile and leave it to concentrate & crystallise???) or SM data processing, beyond the direct methods stuff. I suggest that someone with SM expertise needs to look at and point out some basic points that need inclusion. However, here are my thoughts:

    • Introduction - great.
    • History - seems ok. A good mix, and it does point out that protein Crystallography (PX) evolved from SMX.
    • Scattering Tecs - Seems fine to me - maybe a little PX biased - can an SM-er help out with and example of why SMX is better than say, powder diffraction?
    • Crystallisation - added link to recrystallisation, which has a nice series of diagrams showing how SM xtals are grown - no need to re-invent the wheel, eh?
    • Mounting the Xtal - fine for PX, but I just don't know for SMx - any takers?
    • X-ray source/recording - fine...
    • Data analysis - fine - as mentioned, I've sorted out phasing for SMers - I hope.
    • Diffraction Theory - great - but we don't need to redo stuff that has all ready been done elsewhere...

    Willow - FANTASTIC WORK - If I'm stepping on your toes, let me know - I tend to be a little sporadic as my wiki-time can be variable.

    Keep up the work, editors! Bassophile 11:02, 13 July 2007 (UTC)

    [edit] Suggestions would be very welcome

    As promised, I've returned to work on the History section and would be grateful for constructive criticism and specific suggestions, especially from editors who still feel that the article is unbalanced. I added a bit of chemistry today and will be adding some physics over the next week or so. It would be helpful to know which results from other fields should be added to our description of X-ray crystallography. Once the content is more-or-less agreed upon, we can add all the inline citations and figures. Thanks for your help! :) Willow 21:44, 30 August 2007 (UTC)

    [edit] Useful figures?

    I'd like to come up with a list of Figures that might augment the article. Here are some of my initial thoughts; please give me your ideas on these, and feel free to add more!

    • Contrast between microscope with lenses and X-ray diffraction
    • Density diagram; perhaps a contour plot of a 2D molecule or a 3D shell around a molecule
    • Picture of a crystal and its regular construction
    • Closeup of the unit cell
    • distinction between molecular symmetry and crystal symmetry
    • Intuitive understanding of a Fourier series
    • Phase and amplitude of a Fourier component
    • 2D Fourier series shown as lattice of black dots of different sizes
    • Visualization of the 3D reciprocal space for a crystal
    • Crystalline symmetry
    • Connection between Bragg scattering and Fourier transform; derivation of Bragg law
    • Diagrams of X-ray production devices (tubes/synchrotrons)
    • Diagrams of goniometer, four-circle, kappa diffractometer
    • precession method, oscillation method
    • Good diagram of the Ewald sphere/shell
    • Clarification of the Laue method (broad spectrum) vs. monochromatic X-ray methods
    • Visual explanation of need to rotate >360 degrees to get a complete picture of reciprocal space within a given resolution
    • Disorder, mosaicity, twinning
    • Plot of bond order vs. bond length to illustrate chemistry applications

    I realize this article is getting long and detailed. However, I'd like to get a complete picture of the field before we fork off daughter articles. Thanks for your patience! :) Willow 16:55, 31 August 2007 (UTC)

    Keep up the good work Willow! From the text books I have including the topic:

    • diffraction patterns of different simple materials to show effect of symmetry in original crystals, misalignment of crystal, differnt types of lattice affecting patterns.
    • At least one powder diffraction image.
    • diagram showing how zonal lines come about.
    • Leonhard chart
    • Greninger chart
    • Different shapes of Laue spots and what they mean
    • A diffraction photograph of a metal sample such as copper sheet, or wire (this is a metallurgy application)

    Graeme Bartlett 22:49, 31 August 2007 (UTC)

    [edit] Unbalanced?

    I'm not sure if the template is still necessary, but in any case it was misleading IMO. The template said "This article's representation of one or more viewpoints about a controversial issue may be unbalanced or inaccurate." IMO this is not a controversial issue, but only a matter of missing information and balance. I've replaced it for now with the {{missing information}} template, which I hope will be more accurate and explicit. It says "Concern has been expressed that this article or section is missing information about: minerals and crystals that are not molecular/biological." --Itub 09:01, 18 September 2007 (UTC)

    Thank you, Itub! I would like to ask the people who still feel that the article is unbalanced to lay out a "roadmap" of specific changes or additions they feel are necessary to remove the tag. If they don't reply by, say, 1 October 2007, I'll assume that they're satisfied and will remove the tag. Meanwhile, I'll try to keep improving the article to include more chemical and mineralogical aspects. Dangerously overbalanced ;) Willow 20:41, 19 September 2007 (UTC)

    [edit] Page length

    I've noticed that the article is getting a bit long. The lead is longer than the recommended limit of four paragraphs (it currently has five slightly long paragraphs), and some parts of the article could probably be split out and summarized. I think the easiest one to split out would be the history. --Itub 16:07, 21 September 2007 (UTC)

    Agree that the lead is too long. The material is excellent, but I believe that everything is explained at slightly too much length. Splitting things off should be considered. EdJohnston 16:13, 21 September 2007 (UTC)
    I agree as well, and I'd even prepared a stub, History of X-ray crystallography, for the first daughter article. However, I wanted to get the material clear in my own mind, before I split it into pieces, so that the daughter and mother articles would be consistent. Can you be patient for a week or so? The lead is a little vexing, though; I'm not really sure which paragraph to sacrifice there. Does anyone have a suggestion? Willow 16:20, 21 September 2007 (UTC)

    [edit] Crystallography

    The introductory section of this article is incorrect. X-ray crystallography isn't about the "beam of X-rays being deflected by the crystal." That's what all this nonsense about lattice planes, unit cells, diffraction patterns and the like is about--x-ray crystallography uses the atomic arrangement of a crystal, not the macrostructure. KP Botany 22:42, 22 September 2007 (UTC)

    KP Botany - you are proof positive that no good deed goes unpunished. If you don't like the phrasing of something change it. Every single complaint you've lodged has required a simple rewording. If you are unqualified, then find somebody who is. Let me help: X-ray crystallography determines the physical arrangement of atoms by examining the refraction pattern of incident X-rays on a solid. Incidentally, anybody who reads "atoms" and believes that the article is about the "macrostructure" probably needs to read the wikipedia page about atoms. People who work for free to share your knowledge: good work - the factual accuracy tag is moronic, and I support its removal. --anon138.67.37.79 02:37, 23 September 2007 (UTC)

    Wikipedia:Talk page:"Article talk pages are provided for discussion of the content of articles and the views of reliable published sources. They should not be used by editors as platforms for their personal views." Nor for your personal opinions about me--these can go on user talk pages if they are related to a Wikipedia issue, otherwise they don't belong here period. It's always nice to see editors working so hard on an article that they have the time to use an anony IP to get in a personal attack. I suggest spending the time reading up on x-ray diffraction, instead. KP Botany 17:49, 23 September 2007 (UTC)

    I notice that some authors make a point of distinguishing 'deflected' from 'diffracted.' I would fix the problem noted above by changing the first occurrence of 'deflected' to 'diffracted' and then adding See Also to Dynamical theory of diffraction to show that we understand the physics. However I'm not sure this is exactly what KP Botany is concerned about. I'll make this change and remove the 'Disputed' tag if no-one objects. EdJohnston 06:02, 23 September 2007 (UTC)
    I think we all agree that the scattered X-rays are indeed "deflected" from their original direction, so the sentence per se was not inaccurate. Rather, where we seem to disagree is whether the sentence conveys the right mental picture to a lay-person who reads only the first sentence. With that aim in mind, it's hard to find the right balance between pithiness, technical accuracy and intelligibility. I'd originally thought of using the more technical term "scattered" instead of "deflected", but I was worried that lay-people would not get it, either. The "manner of deflection" was an admittedly imperfect finesse, though, so I've replaced it with my first impulse; "scattering" does convey the idea of multiple scattered beams, which is a bonus. "Diffracted" is good, too, but "scattered" is more general. Hoping that this issue has been resolved and that the mineralogical ones will soon be as well, Willow 13:43, 23 September 2007 (UTC)
    Your new wording seems OK to me. EdJohnston 13:56, 23 September 2007 (UTC)

    Wow. KP Botany 17:49, 23 September 2007 (UTC)

    KP Botany, can you say more? I was uncertain about 'deflected' because it is slightly too vague to be a standard technical term. However your objection, if carefully read, doesn't seem to be appealing to standard physical concepts, so I don't know where it is coming from. The term 'scattering' is just about the most general possible way of referring to what happens when electromagnetic radiation strikes a solid. How are we falling short here? Please cite a physics paper or textbook if you think this is wrong. EdJohnston 23:41, 23 September 2007 (UTC)

    [edit] Factual points of dispute

    The talk page stands as it was when I put the disputed tag back. You have not dealt with the issue that caused the tag to be placed there. Please do so by putting a general introduction into what x-ray crystallography does and how it does it into the article before removing the tag again. KP Botany 02:04, 24 September 2007 (UTC)

    Forgive me for pointing this out, but that is not a disagreement of fact. What is the issue you refer to? Please give specific instances of where the article is factually erroneous, not merely poorly worded in your opinion. Otherwise, the tag should be removed, because there is no dispute of its factual accuracy, right? Willow 02:20, 24 September 2007 (UTC)
    PS. If you review the History section, you'll see that I added some discussion of chemical, metallurgical and mineralogical applications of early X-ray crystallography — not enough perhaps, but some highlights have been hit (feldspar story to come soon). More generally, I have emphasized that any type of crystal structure may be solved, no? Willow 02:25, 24 September 2007 (UTC)
    • "X-ray crystallography is the science of determining the arrangement of atoms within a crystal from the manner in which a beam of X-rays is scattered from the crystal." As I stated above this sentence is incorrect. You cannot determine the atomic structure of a crystal from the way the x-ray beams are "scattered by the crystal." Well, hell, maybe you can. So, point out to me in the article where it explains how you gain the atomic structure of the crystal from x-ray scattering by the crystal itself, how the crystal, rather than its atomic structure scatters x-rays to "produce a three-dimensional picture of the atoms within the crystal, from which their chemical bonds and other information can be derived." Because I just don't see this in the article. Maybe I'm misreading something.
    The article clearly states that the X-rays are scattered from the electrons, and that we are determining the electron density, from which the atomic positions are inferred. The electrons lie within the crystal, so it is accurate to say that the X-rays are scattered from the crystal. As an aside, "scattered from" is not the same as "scattered by". Willow 12:23, 24 September 2007 (UTC)
    • But if that's the case, that scattering an x-ray across the crystal itself is how its done, elaborate upon this method, and develop why scientists went from atomic level planes, and how the wavelength of x-rays enhances the ability to see atoms within a crystal, while scattering them across the crystal itself, rather than those atoms, what face of the crystal you use in different systems, all of that information, because I just can't find it anywhere within the article.
    You seem to mis-understand the technical term "scatter", which is exactly what I feared from lay-people. That's why I used "manner of deflection" originally, although that doesn't convey the multiplicity of the scattered beams. Willow 12:23, 24 September 2007 (UTC)
    • Then elaborate upon full crystal x-ray crystallography and this sentence, "The wavelength of an X-ray is roughly 1 Å (0.1 nm = 10-10 m), which is on the scale of a single atom. Longer wavelength photons (such as ultraviolet radiation) would not have sufficient resolution to determine the atomic positions."
    There's nothing wrong with this sentence, as far as I can see. Are you arguing that UV diffraction from a crystal would allow one to solve for its atomic structure? Or would you like a more thorough definition of the X-ray portion of the spectrum? Willow 12:23, 24 September 2007 (UTC)
    • "For single crystals of sufficient purity and regularity, X-ray diffraction data can determine the positions of most atoms in a crystal structure to within a few tenths of an Ångström."
    This likewise seems correct, although admittedly some structures might be better resolved than that. Even so, they're still "within" a few tenths of an Angstrom. Willow 12:23, 24 September 2007 (UTC)
    • I think what is going on here is that some editors who don't know much about x-ray crystallography, but know some outlier information, have created an article with this information without a fundamental understanding of what the science is and what crystallographers do. The relationships between an x-ray's wavelength and atomic structure of a crystal is fundamental to what one can learn about crystals and molecules using crystallographic techniques. A crystal is NOT its atomic structure, any more than a building is the wood and nails it is built from. You can't learn what type of wood trim is inside the house by looking at the house from the outside, you have to go inside. You use x-ray crystallography to look inside of a crystal or molecule, to look at the regular arrangement of its atoms. This article conveys nothing of this idea. The article is a poorly organized random collection of facts related to doing x-ray crystallography. But it is NOT about x-ray crystallography. All of the time spent disagreeing with me could be spent better going to a library and getting a crystallography book, not a book on crystallography for biologists, or a book on minerals, or a book on protein structures, but a book on crystallography. Couple this with a text on x-ray crystallography, not on physics, and the article can be rewritten. However, I don't have the time to do the research, and I'm not going to add to an article that is a hopelessly unorganized stream of unreferenced facts and inaccuracies. I would have to write the entire article over from scratch. It's a very bad article. Argue with me all you want. It won't make the article accurate or any better than it is. Reading a couple of books could, though. KP Botany 04:06, 24 September 2007 (UTC)
    It would be wise and gracious to not presume too much about my knowledge of crystallography on so limited an acquaintance. You could give me the benefit of the doubt, given that I've added roughly 70kb (most of its current content) to this article. You might also note that working crystallographers have been overall pleased with my contributions.
    As an aside, I'm aware that "atomic structure" does not equal "chemical composition". Having translated Aristotle myself, I know the difference between matter (nails, wood, etc.) and form (the house). I believe that readers of this article will not be confused, either; it clearly spells out that we're solving for the atomic positions.
    From my perspective, your objections are not factual but stylistic; do you agree? I certainly agree that the article is imperfect and incomplete and has a long way to go to FA. But I would appreciate your contributions to it, even as only a gadfly to improve it. Willow 12:23, 24 September 2007 (UTC)
    While I agree that there is poor organization in the body of the article, I fail to understand your objections to the first sentence. Unless you are confusing "determining the arrangement of atoms" with determining the subatomic structure, a claim that the article is not making. Can you please explain your objection more clearly. Rmhermen 04:49, 24 September 2007 (UTC)
    Saying that the crystal doesn't diffract (or scatter) X-rays but the atoms do, is like saying that a mirror doesn't reflect light but its atoms do: semantic hair-splitting that is not necessarily conducive to a concise and clear definition that is intelligible to the general reader. However, if you have a better wording, by all means add it to the article! --Itub 08:04, 24 September 2007 (UTC)
    I think Willow's latest edits are an improvement. And perhaps surface scattering was a source of misunderstanding (I notice a mention by KP Botany of "what face of the crystal you use in different systems" which I didn't understand) Rmhermen 15:44, 24 September 2007 (UTC)

    It's not semantic hair splitting when the fact is crystallography is based upon the relationship between the atomic spacing and the wavelength of x-radiation. And it's bothersome to me that the editors of this article can't seem to grasp or deliver this idea to the audience. A mirror delivers a reflection that can be seen with visible light, understanding a mirror image can be accomplished through simple optical theory without ever getting to the atomic level. X-ray crystallography's foundation depended upon understand the relationship between the lattice structure of a crystal and the wavelength of x-rays. This is NOT semantic hair splitting, this is the underlying theory that directly led to the field. KP Botany 01:32, 27 September 2007 (UTC)

    Can you give us a revised sentence to use in the article? That might help to show where the gap is that you see. I agree that the organization could be better, but that's a longer discussion. EdJohnston 02:15, 27 September 2007 (UTC)
    If I'm understanding aright, perhaps KP would like to see more of the Bragg's law instead of the Fourier transform given in the mathematical derivation? I can appreciate that point of view; Bragg's law is certainly more picturesque, more intuitive, than the Ewald sphere and reciprocal space. We could include a "warm-up" section to the Fourier derivation using Bragg's law, and maybe include a Figure in the main text. I haven't dwelt on Bragg's law much, mainly because it's in the "uncomfortable middle", being too technical for most discussions and not technical enough for others. As usually presented, Bragg's law presupposes that the X-rays are being scattered specularly from uniform sheets of atoms, which even lay-people will recognize as a fiction; for example, they may well ask, "Does the X-ray really scatter from atoms in the same way as from between the atoms?" (Ummm, no.) Bragg's law also doesn't convey the idea of scattering from the electron density, which is more correct (see the Thomson scattering discussion in the article). I further believe that lay-people will find spherical scattering from an electron (the lighthouse metaphor) more plausible than specular reflections from bumpy sheets of atoms. Bragg's law helps to get the unit-cell parameters, but, beyond that, it's not that useful for solving structures (except extremely simple ones) since it doesn't interpret the reflection intensities. However, Bragg's law is useful for lay-people to visualize the constructive interference and it helps to derive the scattering angle for a given spatial frequency component of the electron density, so it might be good as an illustrative middle ground for some readers.
    I agree on the article organization; hitherto I've been more concerned about getting the sections decent than in working on the flow from section to section. What would people prefer? Willow 03:22, 27 September 2007 (UTC)
    In keeping with my idea that separate Method and Applications articles might be the ultimate result, I'd suggest a 'method' article could be written to illustrate Bragg's Law. I agree that the lighthouse metaphor is good, and I think we might show (in a simplified way) how you can get the unit cell parameters and the space group from the pattern of the spots. EdJohnston 04:24, 27 September 2007 (UTC)

    [edit] Article structure

    The lead section of this article is too long (as perhaps is the entire article). WP:Lead would have even an article this long only have a three to four paragraph lead while there are five paragraphs here. Too much is repeated from the lead in the definition section as well. Rmhermen 15:48, 24 September 2007 (UTC)

    Yes, I agree. I'd been willing to let the article and its lead grow longer while I meditated on what should be properly included and what not, but perhaps now is a good time to start trimming. I'm going to try to eliminate the "Definition" section and move straight into the "History section", which outlines some of X-ray crystallography's historical and present-day applications. As you see, I'm still waffling over whether to arrange the material chronologically or by scientific field. Any advice would be most welcome! :) Willow 16:06, 24 September 2007 (UTC)

    [edit] Correct name for this topic?

    The present article, though we are calling it X-ray crystallography, is basically talking about single-crystal X-ray crystallography of biological molecules. I think it should not be too much trouble to fix up the naming later, and it may not be necessary to adjust the scope. If powder diffraction is considered an important topic, I think it can be handled in a separate article. There should not be too much duplication.

    I spent some time looking over one of the cited references today, Glusker, Lewis and Rossi (1994), Crystal Structure Analysis for Chemists and Biologists. Their main distinction was between small molecules and large molecules. They give only a small amount of coverage to powder diffraction. They do NOT make a big distinction between diffraction studies of inorganic and organic molecules, so far as I can tell. Crystals are crystals. Their main focus (in an 854-page book) is not telling people how to do the studies, but how to interpret the results. They have a lot of chapters on applications, i.e., on what has been learned about specific structural problems by X-ray diffraction. They include some inorganic stuff in their application chapters. The point of my comment here is to show that adjusting this article to be sure it addresses small molecules and inorganic problems is probably not a large change. Also, the more recent books on crystallography that I found on the library shelf tend to use 'X-ray crystallography' as a term to cover MOSTLY single-crystal (non-powder) studies and MOSTLY larger molecules. So I don't believe our choice of names is wildly off. EdJohnston 22:14, 24 September 2007 (UTC)

    I'm glad that the name seems OK in the light of references by recognized experts such as Jenny Glusker. Personally, I don't think that the present coverage is overly skewed towards biological molecules, is it? There's a lot about organic and inorganic crystals in the History section. But if you all think it's too much biology, I'd be willing to trim down what remains. Willow 18:45, 25 September 2007 (UTC)
    Before removing good material, I'd be tempted to think about the split between methods and results, i.e. between 'How is it done?', and 'What can be learned from the results?' Glusker et al's book claims (at least) to focus on how to interpret the results. The whole 'Methods' section in our article might one day be split off into a separate article. If we wind up having a 'Results' article it shouldn't be hard to expand its material on the non-biological side, e.g. the borane results that W. Lipscomb got the chemistry prize for. EdJohnston 20:28, 25 September 2007 (UTC)

    [edit] Nobel winners who used X-ray diffraction

    One of the 'to-do' items listed above is 'Better treatment of the historical development.' For your consideration I offer the list of Nobel winners who made use of X-ray diffraction, or advanced the method. This could be made into a table like the one in Nobel Prize in Chemistry but it could be expanded to list one of the molecules that each one studied and its molecular weight. This would probably become a separate article if other people think it is a good idea. Here are the Nobel winners I identified.

    NOBELISTS who worked on X-ray diffraction of solids:

    Max von Laue, Physics 1914 "For his discovery of the diffraction of X-rays by crystals."
    William Henry Bragg and William Lawrence Bragg, Physics 1915 "For their services in the analysis of crystal structure by means of X-rays."
    James D. Watson, Francis Crick, Maurice Wilkins, Physiology or Medicine 1962, "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material"
    Max Perutz and John Kendrew Chemistry 1962, "for their studies of the structures of globular proteins" (e.g. myoglobin)
    Dorothy Crowfoot Hodgkin Chemistry 1964 "for her determinations by X-ray techniques of the structures of important biochemical substances"
    William Lipscomb Chemistry, 1976, "for his studies on the structure of boranes" [other work: structures of enzymes in the 1960s]
    Aaron Klug Chemistry, 1982, "for his development of crystallographic electron microscopy and his structural elucidation of biologically important nucleic acid-protein complexes" [During his career he also used regular X-ray diffraction]
    Roderick MacKinnon Chemistry, 2002 "for discoveries concerning channels in cell membranes"
    Roger D. Kornberg Chemistry, 2006 "for his studies of the molecular basis of eukaryotic transcription"

    Let me know if you think this is a good idea. We could try to fit the material into the present article but it's already quite large. Most likely it should be a separate article. EdJohnston 23:03, 24 September 2007 (UTC)

    This seems like a good list to me, and I agree that it seems best as a separate list that we could link to in the "See also" section. There are a few others you might consider adding, but that can wait until it's an article. Thanks for your good ideas and good edits, Ed! :) Willow 18:39, 25 September 2007 (UTC)

    [edit] Fix the sentence that refers to powder diffraction

    See the comment above by User:Irene Ringworm:

    It also seems that other methods such as powder diffraction are mixed up in this article. In my line of work few people would refer to powder or thin-film diffraction as "crystallography", whereas the single-crystal jocks call themselves "crystallographers".

    My own web searches gave results consistent with her comment. This suggests we might replace the following sentence:

    The term "X-ray crystallography" is also sometimes applied to methods that involve X-ray diffraction from polycrystalline materials, such as powders of small crystals studied by X-ray powder diffraction.

    WITH

    Powders of small crystals can be studied using a method called X-ray powder diffraction, which is not generally referred to as crystallography.

    Comments? EdJohnston 02:41, 25 September 2007 (UTC)

    I surveyed some older textbooks of X-ray crystallography, and many do cover powder diffraction, albeit typically with only a chapter or less. It seems to be used mainly to establish that a substance is (poly)crystalline, and to study its structure when the crystals are too small for single-crystal studies. But both of those applications are a form of crystallography, no? So I would be in favor of keeping the present description, although I don't have strong feelings about it. We could elevate it to a disambiguation in italics over the main article as in
    This article covers the X-ray diffraction of single crystals. For the X-ray diffraction of randomly oriented, polycrystalline samples, see powder diffraction.
    What do you all think? Willow 18:35, 25 September 2007 (UTC)
    If no one has objections, I'll add the italics message above the article in a few days — say, on the 1st? Willow 23:02, 28 September 2007 (UTC)

    [edit] Comments on the new figure caption for Image:Eden.png

    Willow expanded the caption for Image:Eden.png in the section X-ray crystallography#Model building and phase refinement.

    An example of electron density for a protein crystal structure at 2.7 Å resolution. The heavy atoms of an arginine residue (upper left), a tyrosine residue (lower left) and a disulfide bond (upper right, in yellow) are highlighted. The intervening bonds represent the heavy atoms of peptide groups, while the smooth green tube running throughout represents a spline fit to the polypeptide backbone.

    It's fine to provide more detail, but I'd lose the 'heavy atom', which suggests metals. Also if we are going to point everything out, perhaps numbers should be added to the diagram.

    For comparison here's the original caption supplied by Bassophile when he made the diagram:

    An example of electron density contoured at 1 sigma, of a crystal structure solved to 2.7 Å resolution. An Arginine residue (top left), a tyrosine residue (bottom left) and a disulphide bond (right) are highlighted

    The version just preceding Willow's was the same as Bassophile's but with the 'top left' etc. parenthesized directions left out, which I agree are helpful for understanding. I tinkered a bit with new versions of the caption, but I think it's too hard for people to precisely figure out that picture. (There seem to be too many green tubes). Bassophile's caption (with the 'top left' etc included) I think is preferable. Note also there is a slight licensing problem with the image, in that Bassophile wanted to restrict use of the picture to just this article, which I think muddies the GFDL: Permission granted in Xray_Crystallography page - for other uses contact Author. EdJohnston 17:28, 26 September 2007 (UTC)

    How about "non-hydrogen atoms" in place of "heavy atoms"? That's what meant, anyway. It's a little long-winded, but more clear. Willow 23:04, 28 September 2007 (UTC)
    Yes, your new version is better! But instead of 'represent spline fits to the polypeptide backbone' I'd just say 'represent the polypeptide backbone.' Would splines really give such perfect cylinders? EdJohnston 00:06, 29 September 2007 (UTC)
    Sorry, I should've been more clear! The straight green tubes are chemical bonds involving carbon, just as the straight blue and red ones represent bonds to nitrogen and oxygen, respectively. But you'll see two really long curved green tubes that pass near the bases of the tyrosine, arginine and disulfide bond. For example, the upper tube enters the picture at perhaps 2 o'clock in the front, then moves backward and then swoops downwards in the back, although it's a little fuzzy there. The lower tube cuts across the middle, passing through the peptide groups. Those tubes approximate the path of the protein backbone, most likely by a spline fit to the Cα positions; we won't know for sure until Bassophile tells us. If we re-do the figure, I'd be in favor of eliminating them, since they don't correspond to "real" atoms observable in the electron density. If we keep them, we should probably make them a different color, say magenta, to make the caption easier to explain. If we re-do the Figure, though, we might consider doing a different molecule (maybe a non-biological one) with much higher resolution; it'd be nice to be able to contour it so that you see the hole in the aromatic ring, or even the atoms as isolated "blobs". Just a few stray thoughts, Willow 02:50, 29 September 2007 (UTC)


    Sorry about my extended absence. At 2.7A resolution, even tweaking with contouring will not allow you to see the "hole" in the aromatic ring. One would need resolution better than 2A for that - I'll see what I can come up with. If the consensus is to remove the "cartoon" representation ( indeed, a pretty spline-esque fit from C-alpha to C-alpha), I can redo it. Let me know. I can be e-mailed from my userpage.

    90.204.105.203 20:28, 11 October 2007 (UTC) That was me, btw Bassophile 20:31, 11 October 2007 (UTC)

    [edit] Specific tasks to remove "disputed facts" tag

    It'd be helpful to have a clear roadmap to remove the "disputed facts" tag. I'm personally unaware of any incorrect statements in the present article, but I'm perfectly willing to believe that there might be some. It'd be nice to have them listed specifically, all in one place, here in this section, so that we can deal with them one-by-one and strike them from the list, similar to what's done at FAC. Once the disputed facts have been resolved, we can remove the tag. Willow 23:00, 28 September 2007 (UTC)

    [edit] Specific tasks to remove "missing information" tag

    Likewise, it'd be helpful to list specific items of "missing information" that should be added to the article, so that we can add them and remove that tag as well. The spirits are willing, but the direction is weak — or at least Delphic. ;) Willow 23:00, 28 September 2007 (UTC)

    [edit] User:Genisock2 and the tags

    I put these tags here for deficiencies in the article that have yet to be addressed. Namely, the article lacks an outline, a coherent understanable general explantion of the topic and development of the various uses of x-ray crystallography in a logical fashion, such as single crystals, chemistry, proteins, DNA. Don't start an edit war, and don't delete the tags just because chemistry is your area and it covers chemistry. X-ray crystallograpy is used extensively in the materials science industry for quality control, and has been used for this purpose for decades. To ignore it because you're a chemist is fine in your profession, but it's not fine for a Wikipedia article. KP Botany 01:51, 8 October 2007 (UTC)

    not stopping you from writeing about it.Geni 11:37, 8 October 2007 (UTC)
    Real life is. KP Botany 13:59, 8 October 2007 (UTC)

    Geeze, now I'm supposed to believe that hexamethylenetetramine is a rock or what? What is it with you and this article that you don't see how crappy it is, how disorganized it is, and how much it is missing? People will come here and think just like the lot of you that x-ray crystallography is something used by chemists and biologists exclusively. The article is a piece of crap. Good grief, one ionic crystal is used to describe the use of x-ray crystallography in all of materials science and geology?

    Fine, the article is a piece of shit. Put all of you want it this way, and clearly our latest editor owns it enough to declare that a single inganic crystal makes the article perfect.

    Keep the crap. KP Botany 14:04, 8 October 2007 (UTC)

    [edit] Move this article so you can own it in your own space

    This article should be moved to X-ray crystallography (organic) so everyone who thinks that the science is solely used by chemists to study organic molecules and by biologists can have the article that all of you so obviously want. Then it's fine by me to remove the tags. But without the tags, that you are removing without cleaning up this piece of shit, this article needs gone from its current title. Because you're lying to the readers--it's not about X-ray crystallography, it's about organic molecule x-ray crystallography. KP Botany 14:06, 8 October 2007 (UTC)

    [edit] Enough of this shit-- this article stinks, and you know it

    I will not edit a single piece of this article because editors do not want it to be anything other than an article on the x-ray crystallography of organic substances. That is not what x-ray crystallography is, a field limited to organic substances. It is a vast field that includes applications in metallurgy, materials science, crystallography, mineral identification, volcanology and other areas. The editors of this article have focused on minor points in the field without a clear outline of its historic development and the applications. The editor removing the tags is doing so without any knowledge of what is missing, or any concern for the quality of article that editors present to readers. As such is the case, I simply must concede ownership to him/her and his superior knowledge of wikilawyering to get the tags removed from this article at all costs. KP Botany 14:10, 8 October 2007 (UTC)

    There is some discussion of the applications to metallurgy, materials science, and mineral identification, no? There's the sentence, "X-ray crystallography is useful in identifying known materials, characterizing new materials and in discerning materials that appear similar by other experiments." Alloys are discussed, as are distinguishing chemically identical crystals that may appear similar by other probes, e.g., silicates. It's stressed that the method pertains to crystals of any chemical composition, too, right? I honestly don't see that organic and biological crystals get excessive attention; there's also a lot of basic chemistry, e.g., the new forms of metal-metal bonds and resonance stabilization, and all those early structures of inorganic crystals like the rutile/brookite/anatase story and this sentence which provides 10 references to the scientific literature
    “ The structure of diamond was solved in the same year, proving the tetrahedral arrangement of its chemical bonds and showing that the C-C single bond was 1.52 Ångströms. Other early structures included copper, calcium fluoride (CaF2, also known as fluorite), calcite (CaCO3) and pyrite (FeS2) in 1914; spinel (MgAl2O4) in 1915; the rutile and anatase forms of titanium dioxide (TiO2) in 1916; pyrochroite and, by extension, brucite [Mn(OH)2 and Mg(OH)2, respectively] in 1919; and wurtzite (hexagonal ZnS) in 1920. ”
    To be sure, the short "Contributions to mineralogy and metallurgy" section could be expanded slightly, but that seems like too small a failing to call the whole article excrement. What about the lead, the rest of the history, the methods parts, and the Mathematical Derivation? They're not protein/organic centric and they're not completely awful, are they? Willow 16:00, 8 October 2007 (UTC)

    [edit] More collegial tone? ;)

    Wow, I take a little vacation to work on Catullus, and everything goes crazy! Let's all take a little nap, shall we, and then return in a few hours to reach consensus?

    I hope that we agree that this article is not a battle-field, nor a place to posture and needle one other; anyone wanting to do that is encouraged to find another outlet. We're all here to improve the article, right? And we can't do that unless we can articulate what's wrong with it; we need to diagnose its failings and find a cure. All we're asking for is a clearly defined set of criticisms that we can address.

    Personally, I think the article is OK as is, and probably deserves its "B" ranking. It could be a lot better, though; I totally admit that. It suffers from weak flow in its writing and haphazard treatment of sundry topics. I wrote it pretty much single-handedly as part of the May Science Collaboration of the Month (that wasn't), and single-author works are notoriously stilted, especially when the author is no expert. The parts left over from before May are also pretty bad. Nevertheless, I've worked hard to improve the article, and it serves no good purpose to simply dismiss it as excrement. We would all do better if you could just find your voice and articulate exactly what facts are incorrect, what exactly you'd like to have added, how you'd improve the article, and what changes in its organization you'd recommend. Your previous comments, while clearly negative, have been pretty vague; at least they seem so to me. How can we fix the article if you won't tell us what's wrong? I know you can do better; please rise to the occasion now or tell us when you will be able to. Willow 16:00, 8 October 2007 (UTC)

    About all I can see is that the method section assumes that you are in a lab of some sort rather than an industrial setting.Geni 18:19, 8 October 2007 (UTC)
    That would be my bad, as I wrote some of the initial methods bit, and I seem to work in a lab(!). KP Botany is way out of line. Willow has done a great job - Crystallography is a large and conceptually difficult topic, and the article, whilst not perfect (show me a perfect article), defo deserves a B. KP's main beef seems to have been that it was over biological - which it was. Again, my bad I think. Willow has made massive improvements and addressed the whole "its too biological" concern. The whole concept of Wikipedia is that editors edit pages to make them more accurate. The only thing KP has edited is the talk page. If KP wants to include his/her ideas in article, then he/she should go ahead with it. Bassophile 20:40, 11 October 2007 (UTC)
    I seem to be repeating myself...

    "There has been some discussion of this in the past. Most small molecule crystallography seems to have be placed in powder diffraction (yes, I am aware there is a difference!). If you wish to add a section pointing out the differences between small molecule and macromolecular crystallography, such as more emphasis on direct methods, different crystallisation methods etc... go for it (be bold)! Bassophile 14:55, 30 May 2007 (UTC)" Bassophile 20:45, 11 October 2007 (UTC)

    [edit] remove goniometer animation, replace by simple image

    A 10 MB animated .gif, that is not even closely related to X-ray crystallography, takes ages to load and doesn't illustrate the concept much better than an ordinary image with labelled angles. However, I feel the image might be useful in an article on goniometers; it just shouldn't load on default. —Preceding unsigned comment added by 84.161.129.78 (talk) 18:27, 1 March 2008 (UTC)

    [edit] Laue equations

    I'm just wondering if anyone would help spruce up the article on Laue equations? Thanks. Veritas (talk) 01:12, 12 March 2008 (UTC)

    [edit] David Harker

    Can anyone throw any light on this phrase please: "the John Wayne of crystallography" was the description given by Luzzati* of David Harker, the American X-ray crystallographer?

    • Vittorio Luzzati, a crystallographer at the Centre for Molecular Genetics in Gif-sur-Yvette near Paris, France

    thanks,

    nitramrekcap 17:16, 11 April 2008 (UTC)