Thank you all for your comments/references and now I have a better understanding of what could be actually happening. But I have a feeling that disorder, where the twin domains can interfere with each other, is not actually so unusual. And in some cases MR might be possible to reveal a partial structure. (I ran into papers like this before but I couldn't think of one at the top of my head.) Why there is not a package out there to allow refinement against such data? I feel that if you have phase information it is possible to model the translation between different micro-domains...
Sincerely, Chen > On Apr 25, 2014, at 3:21 PM, "Keller, Jacob" <kell...@janelia.hhmi.org> wrote: > > Thanks to all—I’ve got the paper now > > JPK > > From: Keller, Jacob > Sent: Friday, April 25, 2014 1:58 PM > To: 'Oliver Zeldin' > Cc: CCP4BB@jiscmail.ac.uk > Subject: RE: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder > > Does anyone know of a place where one can obtain this reference for free? I > would contact Darwin himself, but I suspect he wouldn’t write back. I think > this is the original paper proposing the mosaic block model, and I’d really > like to see his reasoning. > > Darwin, C. G. (1922). Philos. Mag. 43, 800±829. The reflexion of X-rays from > imperfect crystals > > JPK > > From: oliver.zel...@gmail.com [mailto:oliver.zel...@gmail.com] On Behalf Of > Oliver Zeldin > Sent: Friday, April 25, 2014 1:03 PM > To: Keller, Jacob > Cc: CCP4BB@jiscmail.ac.uk > Subject: Re: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder > > Dear Jacob, > > In terms of the effect of crystal (lattice) defects on diffraction spot > profiles, there are two great papers by Colin Nave that discuss this: > http://journals.iucr.org/d/issues/1998/05/00/issconts.html and > http://journals.iucr.org/d/issues/1998/05/00/issconts.html . There is also > this paper on the nature of mosaic micro-domains: > http://journals.iucr.org/d/issues/2000/08/00/en0024/en0024.pdf. > > I am sure there must be other references for the 'nature' of lattice > disorder, and it anyone can point to them, I would be grateful. > > Cheers, > > Oliver > > > On Fri, Apr 25, 2014 at 6:20 AM, Keller, Jacob <kell...@janelia.hhmi.org> > wrote: > >your Gedankenexperiment on powder diffraction is not correct. You would > >record a powder diffraction pattern if you rotated a single crystal around > >the beam axis and record the result on a single image. > > If you wanted to do it with a single crystal, you would have to rotate the > crystal through all possible rotations in 3d, not just around the axis of the > beam, because you would then miss all the reflections which were not in the > diffraction condition at that phi angle. I agree that it could be done this > way (not sure why this is important though.) > > >This rotation does not affect the mosaicity and the mosaicity of a powder > >sample related only to the mosaicity of the micro crystals present in the > >powder. You also do not get arcs when reducing the powderness but you start > >seeing single spots. This can often be observed in the presence of ice rings. > > You are talking about "powderness," which I would guess is a measure of the > completeness of the sampling of all possible orientations of the constituent > crystals, and I agree with what you say would happen. I said, however, > mosaicity, which is a measure of the breadth of the distribution of the > orientation angles of the microdomains/microcrystals. By decreasing > "powderness," one would do nothing to mosaicity. If one could arrange the > microdomains into some range of orientation angles, one would reduce the > mosaicity, and get arcs. I wish I had a picture of an arc-containing > diffraction pattern--I've seen them from time to time, and they're always of > course bad news. Anyone on the list have such a diffraction pattern handy? > > JPK > > > > > On 04/25/2014 09:32 AM, Keller, Jacob wrote: > > Is the following being neglected? > > > > In a crystal with these putative mosaic microdomains, there will be > > interference between microdomains at their edges/borders (at least), > > but since most microdomains are probably way smaller than the > > coherence length of 3-10 microns, presumably all unit cells in domain > > A interfere with all unit cells in domains B, C, etc, which are in the > > same coherence volume. In fact, as I said too unclearly in a previous > > post, as the putative microdomains become smaller and smaller to the > > limit of one unit cell, they become indistinguishable from unit cell > > parameter variation. So I am becoming increasingly suspicious about > > the existence of microdomains, and wonder what hard evidence there is > > for their existence? > > > > As a thought experiment, one can consider the microdomain theory taken > > to its limit: a powder diffraction image. In powder diffraction, there > > are so many crystals (read: microdomains) that each spot is manifested > > at its Bragg angle at every possible radial position on the detector. > > Mosaicity would be, what, 360 degrees? > > So, now imagine decreasing the mosaicity to lower values, and one gets > > progressively shorter arcs which at lower values become spots. > > Doesn’t this mean that the contribution from microdomain mosaicity > > should be to make the spots more like arcs, as we sometimes see in > > terrible diffraction patterns, and not just general broadening of > > spots? Put another way: mosaicity should broaden spots in the radial > > direction (arcs), and unit cell parameter variation should produce > > straight broadening in the direction of the unit cell variation of > > magnitude proportional to the degree of variation in that direction. > > > > JPK > > > > > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > > Ian Tickle Sent: Thursday, April 24, 2014 7:01 PM To: > > CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] Twinning VS. > > Disorder > > > > > > Dear Herman On 24 April 2014 22:32, > > <herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com>> > > wrote: > > > > The X-ray coherent length is depending on the crystal, not the > > synchrotron and my gut feeling is that it is at least several hundred > > unit cells, but here other experts may correct me. > > > > > > I assume you meant that the coherence length is a property of the beam > > (e.g. for a Cu target source it's related to the lifetime of the > > excited Cu K-alpha state), not the crystal, e,g, see > > http://www.aps.anl.gov/Users/Meeting/2010/Presentations/WK2talk_Vartan > > iants.pdf (slides 8-11). The relevant property of the crystal is the > > size of the microdomains. You don't get interference because > > coherence length << domain size, i.e. the beam is not coherent over > > more than > > 1 domain. This is true for in-house sources & synchrotrons, I guess > > for FELs it's different, i.e. much greater coherence length? > > This relates to a question I asked on the BB some time ago: if the > > coherence length is long enough would you start to see the effects of > > interference in twinned crystals, i.e. would the summation of > > intensities break down? I defer to the experts on synchrotrons & FELs! > > Cheers -- Ian > > > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Icedove - http://www.enigmail.net/ > > iD8DBQFTWiJpUxlJ7aRr7hoRAvhpAKCWt3PwAQsPnUgMlHjYoGS/7lVlGACglWpz > K+rZPikLZBwe+CrK29WhBnc= > =4a9F > -----END PGP SIGNATURE----- > > > > -- > Dr. Oliver B. Zeldin > Brunger Group > Stanford University
