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> [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<mailto: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<mailto: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<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of > Ian Tickle Sent: Thursday, April 24, 2014 7:01 PM To: > CCP4BB@JISCMAIL.AC.UK<mailto: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><mailto: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
