Re: [ccp4bb] Strange spots
Dear All, I posted some odd diffraction late last year consisting of Bragg diffraction spots with a diffuse ring or halo. Along with Richard Welberry at ANU we have now published an explanation for this diffuse scattering. For those that are interested the reference is:- Acta Cryst. (2011). B67, 516-524 [ doi:10.1107/S0108768111037542 ] Diffuse scattering resulting from macromolecular frustration T. R. Welberry, A. P. Heerdegen, D. C. Goldstone and I. A. Taylor Kind Regards David -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA
Re: [ccp4bb] Strange spots
Dear All, Thank you for the replies sorry about the delay in my reply. Here is some more information, for those of you that are interested, to try fill in some gaps. The data was collected on our home source with osmic vairmax-HF optics and an RAXISIV++ detector. We are investigating whether it is an optics issue but this is unlikely as other crystals in the screening run didn't display this phenomenon. The crystal was grown in the presence of 12% glycerol and transfered to 20% glycerol as a cryo. I haven't tried other cryos as crystals also grow in 20% glycerol and do not require further cryoprotectant. I have uploaded a movie showing a wedge of data showing how the circles around the spots progress. http://www.4shared.com/video/o8_YmInD/Spot_defect.html (~12mb download) The crystals index and scale in p6122 (a=b=73, c=110) with a single monomer in the ASU (by matthews, 45% solvent). We do however see a peak in the native patterson at (0,0,0.2 ~50% origin height). Cheers Dave On 29/10/2010 17:08, David Goldstone wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA
Re: [ccp4bb] Strange spots
Dear David, Many thanks indeed for this movie and the extra info. It is quite captivating! The 'strange spot' features do seem progress to other regions of reciprocal space at approximately constant diffraction resolution in an anti-clockwise manner.but I am still digesting your movie Behind the scenes discussion, between Colin Nave, James Holton and myself, has been going on. Since Colin has been the main leader in these I leave it to Colin to take it up from here and I can chip in if I can add anything. Greetings, John On Wed, Nov 3, 2010 at 3:53 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Thank you for the replies sorry about the delay in my reply. Here is some more information, for those of you that are interested, to try fill in some gaps. The data was collected on our home source with osmic vairmax-HF optics and an RAXISIV++ detector. We are investigating whether it is an optics issue but this is unlikely as other crystals in the screening run didn't display this phenomenon. The crystal was grown in the presence of 12% glycerol and transfered to 20% glycerol as a cryo. I haven't tried other cryos as crystals also grow in 20% glycerol and do not require further cryoprotectant. I have uploaded a movie showing a wedge of data showing how the circles around the spots progress. http://www.4shared.com/video/o8_YmInD/Spot_defect.html (~12mb download) The crystals index and scale in p6122 (a=b=73, c=110) with a single monomer in the ASU (by matthews, 45% solvent). We do however see a peak in the native patterson at (0,0,0.2 ~50% origin height). Cheers Dave On 29/10/2010 17:08, David Goldstone wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA -- Professor John R Helliwell DSc
Re: [ccp4bb] Strange spots
Is it known/can you divulge the nature/structure of the macromolecules in the crystal? Is it protein, nucleic acid, other? Does the structure have periodicity to it? JPK - Original Message - From: David Goldstone david.goldst...@nimr.mrc.ac.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, November 03, 2010 10:53 AM Subject: Re: [ccp4bb] Strange spots Dear All, Thank you for the replies sorry about the delay in my reply. Here is some more information, for those of you that are interested, to try fill in some gaps. The data was collected on our home source with osmic vairmax-HF optics and an RAXISIV++ detector. We are investigating whether it is an optics issue but this is unlikely as other crystals in the screening run didn't display this phenomenon. The crystal was grown in the presence of 12% glycerol and transfered to 20% glycerol as a cryo. I haven't tried other cryos as crystals also grow in 20% glycerol and do not require further cryoprotectant. I have uploaded a movie showing a wedge of data showing how the circles around the spots progress. http://www.4shared.com/video/o8_YmInD/Spot_defect.html (~12mb download) The crystals index and scale in p6122 (a=b=73, c=110) with a single monomer in the ASU (by matthews, 45% solvent). We do however see a peak in the native patterson at (0,0,0.2 ~50% origin height). Cheers Dave On 29/10/2010 17:08, David Goldstone wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Strange spots
OK! John prompted me to look more carefully at the images and they don't seem to be consistent with any optics or detector effect. Attached a Blowup (almost as strange as Antonioni's 1966 film with this name) of one of the areas. As others have pointed out already, the features are not round halos surrounding the spots though they look like this at first glance. They seem to consist of fuzzier subsidiary spots. If these spots were oriented in a 6 fold manner, this would, I think be consistent with a commensurate modulation with q=0.5a* (assuming the subsidiary spots are half way between the main spots). However, there seems to be some evidence that the subsidiary spots around each main spot are 30 degrees apart not 60 degrees. A bit difficult to see though. Looking at the movie, I think they are most visible for zones with constant l (h and k varying) though they presumably occur elsewhere. I presume the indexing would reveal this. It might be worth trying to index on a supercell with a=146A and see if there is anything left. Regards Colin -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of John R Helliwell Sent: 03 November 2010 17:00 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots Dear David, Many thanks indeed for this movie and the extra info. It is quite captivating! The 'strange spot' features do seem progress to other regions of reciprocal space at approximately constant diffraction resolution in an anti-clockwise manner.but I am still digesting your movie Behind the scenes discussion, between Colin Nave, James Holton and myself, has been going on. Since Colin has been the main leader in these I leave it to Colin to take it up from here and I can chip in if I can add anything. Greetings, John On Wed, Nov 3, 2010 at 3:53 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Thank you for the replies sorry about the delay in my reply. Here is some more information, for those of you that are interested, to try fill in some gaps. The data was collected on our home source with osmic vairmax-HF optics and an RAXISIV++ detector. We are investigating whether it is an optics issue but this is unlikely as other crystals in the screening run didn't display this phenomenon. The crystal was grown in the presence of 12% glycerol and transfered to 20% glycerol as a cryo. I haven't tried other cryos as crystals also grow in 20% glycerol and do not require further cryoprotectant. I have uploaded a movie showing a wedge of data showing how the circles around the spots progress. http://www.4shared.com/video/o8_YmInD/Spot_defect.html (~12mb download) The crystals index and scale in p6122 (a=b=73, c=110) with a single monomer in the ASU (by matthews, 45% solvent). We do however see a peak in the native patterson at (0,0,0.2 ~50% origin height). Cheers Dave On 29/10/2010 17:08, David Goldstone wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA -- Professor John R Helliwell DSc attachment: odd_spots_edited.png
Re: [ccp4bb] Strange spots
I don't think it looks like satellite spots at all--it looks more like a flat diffuse scattering background or perhaps a diffuse ring, with some strange blanking/clearing of a circle around the spot. Perhaps it is a result of having not just the usual convolution of the molecule with the lattice, but an added level of a small number (say tens to hundreds) of similar microcrystals within the crystal, whose diffraction is also part of the convolution, but whose small number results in broadening of the spots, making Airy disks? Look at the attached image for what I found on wiki diffraction (http://en.wikipedia.org/wiki/Diffraction): Airy disks around stars, which look pretty exactly like our diffraction spots. Same phenomenon? The caption for the image is The Airy disk around each of the stars from the 2.56 m telescope aperture can be seen in this lucky image of the binary star zeta Boötis. I have not convinced myself, however, that the small number of crystals (my suggestion) could make Airy disks. Maybe the pin, or something else, got in the way? JPK - Original Message - From: Colin Nave colin.n...@diamond.ac.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, November 03, 2010 12:52 PM Subject: Re: [ccp4bb] Strange spots OK! John prompted me to look more carefully at the images and they don't seem to be consistent with any optics or detector effect. Attached a Blowup (almost as strange as Antonioni's 1966 film with this name) of one of the areas. As others have pointed out already, the features are not round halos surrounding the spots though they look like this at first glance. They seem to consist of fuzzier subsidiary spots. If these spots were oriented in a 6 fold manner, this would, I think be consistent with a commensurate modulation with q=0.5a* (assuming the subsidiary spots are half way between the main spots). However, there seems to be some evidence that the subsidiary spots around each main spot are 30 degrees apart not 60 degrees. A bit difficult to see though. Looking at the movie, I think they are most visible for zones with constant l (h and k varying) though they presumably occur elsewhere. I presume the indexing would reveal this. It might be worth trying to index on a supercell with a=146A and see if there is anything left. Regards Colin -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of John R Helliwell Sent: 03 November 2010 17:00 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots Dear David, Many thanks indeed for this movie and the extra info. It is quite captivating! The 'strange spot' features do seem progress to other regions of reciprocal space at approximately constant diffraction resolution in an anti-clockwise manner.but I am still digesting your movie Behind the scenes discussion, between Colin Nave, James Holton and myself, has been going on. Since Colin has been the main leader in these I leave it to Colin to take it up from here and I can chip in if I can add anything. Greetings, John On Wed, Nov 3, 2010 at 3:53 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Thank you for the replies sorry about the delay in my reply. Here is some more information, for those of you that are interested, to try fill in some gaps. The data was collected on our home source with osmic vairmax-HF optics and an RAXISIV++ detector. We are investigating whether it is an optics issue but this is unlikely as other crystals in the screening run didn't display this phenomenon. The crystal was grown in the presence of 12% glycerol and transfered to 20% glycerol as a cryo. I haven't tried other cryos as crystals also grow in 20% glycerol and do not require further cryoprotectant. I have uploaded a movie showing a wedge of data showing how the circles around the spots progress. http://www.4shared.com/video/o8_YmInD/Spot_defect.html (~12mb download) The crystals index and scale in p6122 (a=b=73, c=110) with a single monomer in the ASU (by matthews, 45% solvent). We do however see a peak in the native patterson at (0,0,0.2 ~50% origin height). Cheers Dave On 29/10/2010 17:08, David Goldstone wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA -- Professor John R Helliwell DSc *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** attachment: Zboo_lucky_image_1pc.png
Re: [ccp4bb] Strange spots
Dear Jurgen and Petr, I looked at the Princeton incommensurate link kindly provided by Petr. I see your point ie examples of a grouping of subsidiary spots around a central spot. But not continuous circles. I have now checked the Atlas of Optical Transforms (my office copy en route to Manchester United versus Tottenham Hotspur yesterday evening). Little help there. I also looked at Richard Welberry's Diffuse Scattering book (OUP/IUCr Monograph). This has a variety of circular-continuous halo effects from inorganic, and one organic, crystals and explanations of the crystal disorders they arise from; these halo effects seem identical to David Goldstone's.The main difference of the Welberry examples versus the David Goldstone example is the latter is restricted to one part of reciprocal space, at least from the one pattern shown. Basically we need more info from David Goldstone re the fidelity of his detector, pointed out in the earlier discussions as well, and/or more diffraction patterns, ideally as a movie clip of patterns as his crystal is rotated. Greetings, John On Sat, Oct 30, 2010 at 5:06 PM, Jürgen Bosch jubo...@jhsph.edu wrote: I second Petr's opinion. These halos are different compared to John's book. Strong reflections look perfect as can be seen in the red zoomed area. weaker spots show the halos because the crystal lattice was disordered (or because the crystals grew in a disordered or incommensurate fashion). If you increase the contrast of the image you can see more of those halos which have a sharp straight edge pointing at ~six corners around the spots. The usual questions: 1. how does the diffraction look like at room temperature in capillaries ? 2. have you played with more than three different cryo's ? And what was the result of it ? 3. Is my assumption right, that you tried to freeze a large crystal ? Try freezing a smaller one e.g. 50 µm and see how your high resolutions spots behave. The rings we see are the typical remains of weak ice rings ? Then you really should improve your cryo. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Oct 29, 2010, at 4:14 PM, Leiman Petr wrote: I think this is a poly-crystalline incommensurately modulated crystal, i.e. incommensurately modulated crystal, which fractured upon freezing, resulting in averaging of satellite spots. Fig. 3b from here: http://www.princeton.edu/~actin/documents/Proteincrystalscanbeincommensurate lymodulated.pdf Petr On 10/29/10 6:08 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- Professor John R Helliwell DSc
Re: [ccp4bb] Strange spots
The detector issue could be resolved by moving it to a different distance and recording the pattern again. In the absence of further info, my vote goes for James Holton's explanation - the effect could be due to optocal misaligenment Colin -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of John R Helliwell Sent: 31 October 2010 12:47 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots Dear Jurgen and Petr, I looked at the Princeton incommensurate link kindly provided by Petr. I see your point ie examples of a grouping of subsidiary spots around a central spot. But not continuous circles. I have now checked the Atlas of Optical Transforms (my office copy en route to Manchester United versus Tottenham Hotspur yesterday evening). Little help there. I also looked at Richard Welberry's Diffuse Scattering book (OUP/IUCr Monograph). This has a variety of circular-continuous halo effects from inorganic, and one organic, crystals and explanations of the crystal disorders they arise from; these halo effects seem identical to David Goldstone's.The main difference of the Welberry examples versus the David Goldstone example is the latter is restricted to one part of reciprocal space, at least from the one pattern shown. Basically we need more info from David Goldstone re the fidelity of his detector, pointed out in the earlier discussions as well, and/or more diffraction patterns, ideally as a movie clip of patterns as his crystal is rotated. Greetings, John On Sat, Oct 30, 2010 at 5:06 PM, Jürgen Bosch jubo...@jhsph.edu wrote: I second Petr's opinion. These halos are different compared to John's book. Strong reflections look perfect as can be seen in the red zoomed area. weaker spots show the halos because the crystal lattice was disordered (or because the crystals grew in a disordered or incommensurate fashion). If you increase the contrast of the image you can see more of those halos which have a sharp straight edge pointing at ~six corners around the spots. The usual questions: 1. how does the diffraction look like at room temperature in capillaries ? 2. have you played with more than three different cryo's ? And what was the result of it ? 3. Is my assumption right, that you tried to freeze a large crystal ? Try freezing a smaller one e.g. 50 µm and see how your high resolutions spots behave. The rings we see are the typical remains of weak ice rings ? Then you really should improve your cryo. Jürgen - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/ On Oct 29, 2010, at 4:14 PM, Leiman Petr wrote: I think this is a poly-crystalline incommensurately modulated crystal, i.e. incommensurately modulated crystal, which fractured upon freezing, resulting in averaging of satellite spots. Fig. 3b from here: http://www.princeton.edu/~actin/documents/Proteincrystalscanbeincommen surate lymodulated.pdf Petr On 10/29/10 6:08 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- Professor John R Helliwell DSc
Re: [ccp4bb] Strange spots - In book of John Helliwell
I have seen such features myself from time to time on diffraction pictures recorded on X-ray films in the far past and was explaining them by the presence of electron diffraction as they resemble electron diffraction patterns. Source of focused electron beam during X-ray diffraction experiment is a different story. I have no explanation for that. BTW1 when we started to use area detectors, these features disappeared. However features David Goldstone showing us is something else. We never have seen such things before. I would try to take a similar picture on X-ray film. But maybe why to bother?. Unfortunately to be a genius of X-ray diffraction physics in the present MX world will fast convert a person to homeless. My question to John Goldstone: Is it intermittent, of for certain crystal/station/detector you always get that? BTW2 I feel in contemptuous reaction of the community deep discontent of all of us.What? even diffraction physics we do not understand in depth? Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 29, 2010, at 23:23 , Charles W. Carter, Jr wrote: Hi Gérard, I actually bought John's book some time ago and can provide page 321 (attached). I think perhaps John is exaggerating his case, although as I have frequently made similarly inflated claims, I am sympathetic. Here is the pdf file. If it does not go through the CCP4 filters, I would be happy to send it to the first few who request it. Charlie p321.PDF On Oct 29, 2010, at 11:03 PM, Gerard Bricogne wrote: Dear Liz, You will be disappointed. I went immediately to that link, but page 321 is not available as part of the Googlebook sample, which jumps directly from page 320 to page 325. With best wishes, Gerard. -- On Fri, Oct 29, 2010 at 09:13:27PM +0100, elizabeth.d...@diamond.ac.uk wrote: There is always hope!!! Seriously though, I have never seen anything like this before! I am watching this thread with interest to see what others suggest. THanks Also thanks should go specifically to Julian Nomme who took the trouble to send us all the Helliwell book link. Liz From: CCP4 bulletin board on behalf of Sanishvili, Ruslan Sent: Fri 29/10/2010 21:08 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots C'mon now! Everybody knows that frogs in real space become handsome princes in the reciprocal one... N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller Sent: Friday, October 29, 2010 3:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots Yes, but the question is what in real space gives rise to reciprocal-space frog spawn? (Frogs, I guess?) - Original Message - From: Marcus Winter mailto:marcus.win...@agilent.com To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, October 29, 2010 2:56 PM Subject: Re: [ccp4bb] Strange spots Dear David, Further to the previous learned responses, surely, this is just frog spawn ? My apologies: it is a Friday evening, after all... Marcus Winter. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of David Goldstone Sent: 29 October 2010 17:08 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Strange spots Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Strange spots
Fig from John (I have a copy of his book in the office and will see it only tomorrow) due to better quality makes it clear (at least for me) that we see the similar effect shown by David Goldstone. Dr Felix Frolow Professor of Structural Biology and Biotechnology Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Oct 30, 2010, at 10:16 , John R Helliwell wrote: Dear Colleagues, Here is scan of a portion of Fig 8.1b, including a zoom in, as per my earlier email. This was recorded on photographic film, which hopefully removes the worry about whether Dave's detector was malfunctioning, and secondly, being Laue, a simple X-ray optic set up (I have to check if it included a focussing X-ray mirror or not). Even if there is no sure explanation of such halo features, although I did declare 'defects in the crystal' as a possibility, we know in this case that these features were radiation sensitive. Best wishes, John On Fri, Oct 29, 2010 at 5:08 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA -- Professor John R Helliwell DSc diffuse spots 3.jpgdiffuse spots 2 .jpg
Re: [ccp4bb] Strange spots
Dear Dave, You have a collector's item there! The closest I have seen is illustrated in my book 'Macromolecular Crystallography with Synchrotron Radiation' page 321, which is a small molecule example. Best wishes, John Prof John R Helliwell DSc On Fri, Oct 29, 2010 at 5:08 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA -- Professor John R Helliwell DSc
Re: [ccp4bb] Strange spots
Dear John, Would it be possible to know more about what you are referring to without having to buy (or steal) your book :-)) ? Thank you in advance! With best wishes, Gerard. -- On Fri, Oct 29, 2010 at 06:41:51PM +0100, John R Helliwell wrote: Dear Dave, You have a collector's item there! The closest I have seen is illustrated in my book 'Macromolecular Crystallography with Synchrotron Radiation' page 321, which is a small molecule example. Best wishes, John Prof John R Helliwell DSc On Fri, Oct 29, 2010 at 5:08 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA -- Professor John R Helliwell DSc -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Strange spots
Dear Gerard I will do a scan of fig 8.1b asap, probably Monday. Greetings, John Sent from my iPad On 29 Oct 2010, at 18:44, Gerard Bricogne g...@globalphasing.com wrote: Dear John, Would it be possible to know more about what you are referring to without having to buy (or steal) your book :-)) ? Thank you in advance! With best wishes, Gerard. -- On Fri, Oct 29, 2010 at 06:41:51PM +0100, John R Helliwell wrote: Dear Dave, You have a collector's item there! The closest I have seen is illustrated in my book 'Macromolecular Crystallography with Synchrotron Radiation' page 321, which is a small molecule example. Best wishes, John Prof John R Helliwell DSc On Fri, Oct 29, 2010 at 5:08 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA -- Professor John R Helliwell DSc -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Strange spots
Google books: http://books.google.com/books?id=RqNb241Q484Cprintsec=frontcoverdq=Macromolecular+Crystallography+with+Synchrotron+Radiationhl=enei=JA3LTMe2NMSnnQfAjN3mDwsa=Xoi=book_resultct=resultresnum=1ved=0CC8Q6AEwAA#v=onepageqf=false http://books.google.com/books?id=RqNb241Q484Cprintsec=frontcoverdq=Macromolecular+Crystallography+with+Synchrotron+Radiationhl=enei=JA3LTMe2NMSnnQfAjN3mDwsa=Xoi=book_resultct=resultresnum=1ved=0CC8Q6AEwAA#v=onepageqf=false Julian On 10/29/10 1:01 PM, Jrh wrote: Dear Gerard I will do a scan of fig 8.1b asap, probably Monday. Greetings, John Sent from my iPad On 29 Oct 2010, at 18:44, Gerard Bricogneg...@globalphasing.com wrote: Dear John, Would it be possible to know more about what you are referring to without having to buy (or steal) your book :-)) ? Thank you in advance! With best wishes, Gerard. -- On Fri, Oct 29, 2010 at 06:41:51PM +0100, John R Helliwell wrote: Dear Dave, You have a collector's item there! The closest I have seen is illustrated in my book 'Macromolecular Crystallography with Synchrotron Radiation' page 321, which is a small molecule example. Best wishes, John Prof John R Helliwell DSc On Fri, Oct 29, 2010 at 5:08 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA -- Professor John R Helliwell DSc -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Strange spots
Gerard, I happen to have inherited a copy of Sir John's book from Joe Becker some years ago. Don't get your hopes up as the effect is apparently unexplained: No satisfactory explanation for these features has yet been found, but they are probably related to defects in the crystal lattice. Perhaps it is useful to think of the function (Bessel?) that when convoluted with the lattice and molecular transform, would give rise to this phenomenon. It would be interesting to see if, on very long exposure, a second concentric ring appeared further out from the spot. Best- Steve -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Julian Nomme Sent: Friday, October 29, 2010 2:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots Google books: http://books.google.com/books?id=RqNb241Q484Cprintsec=frontcoverdq=Mac romolecular+Crystallography+with+Synchrotron+Radiationhl=enei=JA3LTMe2 NMSnnQfAjN3mDwsa=Xoi=book_resultct=resultresnum=1ved=0CC8Q6AEwAA#v= onepageqf=false http://books.google.com/books?id=RqNb241Q484Cprintsec=frontcoverdq=Ma cromolecular+Crystallography+with+Synchrotron+Radiationhl=enei=JA3LTMe 2NMSnnQfAjN3mDwsa=Xoi=book_resultct=resultresnum=1ved=0CC8Q6AEwAA#v =onepageqf=false Julian On 10/29/10 1:01 PM, Jrh wrote: Dear Gerard I will do a scan of fig 8.1b asap, probably Monday. Greetings, John Sent from my iPad On 29 Oct 2010, at 18:44, Gerard Bricogneg...@globalphasing.com wrote: Dear John, Would it be possible to know more about what you are referring to without having to buy (or steal) your book :-)) ? Thank you in advance! With best wishes, Gerard. -- On Fri, Oct 29, 2010 at 06:41:51PM +0100, John R Helliwell wrote: Dear Dave, You have a collector's item there! The closest I have seen is illustrated in my book 'Macromolecular Crystallography with Synchrotron Radiation' page 321, which is a small molecule example. Best wishes, John Prof John R Helliwell DSc On Fri, Oct 29, 2010 at 5:08 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA -- Professor John R Helliwell DSc -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * === Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
Re: [ccp4bb] Strange spots
Dear David, Further to the previous learned responses, surely, this is just frog spawn ? My apologies: it is a Friday evening, after all... Marcus Winter. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of David Goldstone Sent: 29 October 2010 17:08 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Strange spots Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA
Re: [ccp4bb] Strange spots
Yes, but the question is what in real space gives rise to reciprocal-space frog spawn? (Frogs, I guess?) - Original Message - From: Marcus Winter To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, October 29, 2010 2:56 PM Subject: Re: [ccp4bb] Strange spots Dear David, Further to the previous learned responses, surely, this is just frog spawn ? My apologies: it is a Friday evening, after all... Marcus Winter. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of David Goldstone Sent: 29 October 2010 17:08 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Strange spots Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Strange spots
C'mon now! Everybody knows that frogs in real space become handsome princes in the reciprocal one... N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller Sent: Friday, October 29, 2010 3:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots Yes, but the question is what in real space gives rise to reciprocal-space frog spawn? (Frogs, I guess?) - Original Message - From: Marcus Winter mailto:marcus.win...@agilent.com To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, October 29, 2010 2:56 PM Subject: Re: [ccp4bb] Strange spots Dear David, Further to the previous learned responses, surely, this is just frog spawn ? My apologies: it is a Friday evening, after all... Marcus Winter. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of David Goldstone Sent: 29 October 2010 17:08 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Strange spots Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Strange spots
Only when you do refinement(explains other thread about the unexplained R-gap) JPK - Original Message - From: Sanishvili, Ruslan To: Jacob Keller ; CCP4BB@JISCMAIL.AC.UK Sent: Friday, October 29, 2010 3:08 PM Subject: RE: [ccp4bb] Strange spots C'mon now! Everybody knows that frogs in real space become handsome princes in the reciprocal one. N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov -- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller Sent: Friday, October 29, 2010 3:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots Yes, but the question is what in real space gives rise to reciprocal-space frog spawn? (Frogs, I guess?) - Original Message - From: Marcus Winter To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, October 29, 2010 2:56 PM Subject: Re: [ccp4bb] Strange spots Dear David, Further to the previous learned responses, surely, this is just frog spawn ? My apologies: it is a Friday evening, after all... Marcus Winter. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of David Goldstone Sent: 29 October 2010 17:08 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Strange spots Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Strange spots
I think this is a poly-crystalline incommensurately modulated crystal, i.e. incommensurately modulated crystal, which fractured upon freezing, resulting in averaging of satellite spots. Fig. 3b from here: http://www.princeton.edu/~actin/documents/Proteincrystalscanbeincommensurate lymodulated.pdf Petr On 10/29/10 6:08 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave
Re: [ccp4bb] Strange spots
There is always hope!!! Seriously though, I have never seen anything like this before! I am watching this thread with interest to see what others suggest. THanks Also thanks should go specifically to Julian Nomme who took the trouble to send us all the Helliwell book link. Liz From: CCP4 bulletin board on behalf of Sanishvili, Ruslan Sent: Fri 29/10/2010 21:08 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots C'mon now! Everybody knows that frogs in real space become handsome princes in the reciprocal one... N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller Sent: Friday, October 29, 2010 3:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots Yes, but the question is what in real space gives rise to reciprocal-space frog spawn? (Frogs, I guess?) - Original Message - From: Marcus Winter mailto:marcus.win...@agilent.com To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, October 29, 2010 2:56 PM Subject: Re: [ccp4bb] Strange spots Dear David, Further to the previous learned responses, surely, this is just frog spawn ? My apologies: it is a Friday evening, after all... Marcus Winter. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of David Goldstone Sent: 29 October 2010 17:08 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Strange spots Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Strange spots
On Friday, October 29, 2010 12:59:40 pm Jacob Keller wrote: Yes, but the question is what in real space gives rise to reciprocal-space frog spawn? (Frogs, I guess?) You may laugh, but the Google finds hits on the topic here: http://www.ph.surrey.ac.uk/newsite/ugrad_uploads/Lisowski2004May04100954.pdf and here: http://www.freshpatents.com/Manganese-ozone-decomposition-catalysts-and-process-for-its-preparation-dt20070315ptan20070060472.php?type=description and here: http://atlas-conferences.com/cgi-bin/abstract/cauu-47 Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Strange spots
Autoindexing in the truest sense of the word? ;-) On 10/29/10 12:08 PM, David Goldstone david.goldst...@nimr.mrc.ac.uk wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA
Re: [ccp4bb] Strange spots
On Fri, Oct 29, 2010 at 4:25 PM, Ethan Merritt merr...@u.washington.edu wrote: You may laugh, but the Google finds hits on the topic here: http://atlas-conferences.com/cgi-bin/abstract/cauu-47 anyone who made complete sense of that abstract is invited to go here : http://snarxiv.org/vs-arxiv/ and if you do, please let us know if you needed to apply the Ads/CFT correspondence.
Re: [ccp4bb] Strange spots
Dear Liz, You will be disappointed. I went immediately to that link, but page 321 is not available as part of the Googlebook sample, which jumps directly from page 320 to page 325. With best wishes, Gerard. -- On Fri, Oct 29, 2010 at 09:13:27PM +0100, elizabeth.d...@diamond.ac.uk wrote: There is always hope!!! Seriously though, I have never seen anything like this before! I am watching this thread with interest to see what others suggest. THanks Also thanks should go specifically to Julian Nomme who took the trouble to send us all the Helliwell book link. Liz From: CCP4 bulletin board on behalf of Sanishvili, Ruslan Sent: Fri 29/10/2010 21:08 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots C'mon now! Everybody knows that frogs in real space become handsome princes in the reciprocal one... N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller Sent: Friday, October 29, 2010 3:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots Yes, but the question is what in real space gives rise to reciprocal-space frog spawn? (Frogs, I guess?) - Original Message - From: Marcus Winter mailto:marcus.win...@agilent.com To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, October 29, 2010 2:56 PM Subject: Re: [ccp4bb] Strange spots Dear David, Further to the previous learned responses, surely, this is just frog spawn ? My apologies: it is a Friday evening, after all... Marcus Winter. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of David Goldstone Sent: 29 October 2010 17:08 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Strange spots Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu ***
Re: [ccp4bb] Strange spots
Hi Dave, The circles are quite prominent in the inner circle (lune) that you highlight but not in the next one. The full image is too small to see details but I don't see any clear circular halos for any of the other lunes. If you start with the lune going through the origin and number it zero, then the one with the halos is lune 7. Any chance that there is a pseudo translation with a periodicity of ~1/7th of the reciprocal vector perpendicular to the planes that form the lunes. The pseudo-2D lattice with the halos suggest hexagonal/trigonal/rhombohedral lattice and the halo radius is half the reciprocal unit cell length. Maybe you have some weird stacked rhombohedral packing where two or more rhombohedral cells intercalate so that there are pure rhombohedral unit cell axes that apply to all atoms and some pseudo translations that related an atom in one rhombohedral lattice to one in another stacked lattice. Don't know if that makes sense. It would be interesting to see some images before and after this one. Are the halos circles in reciprocal space or spheres that just look like circles on the oscillation image because the intersection of a sphere with the Ewald sphere looks like a circle. On images where the 6th, 5th etc lune forms a 2D lattice do you see the halo's or is it only on the 7th. As John said you may well have a collectors item but it would sure be nice to know what caused this even if structure determination is not in the cards. Bart On 10-10-29 10:08 AM, David Goldstone wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- Bart Hazes (Associate Professor) Dept. of Medical Microbiology Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax:1-780-492-7521
Re: [ccp4bb] Strange spots
Are these very strong reflections? Do they appear on more than one image? Are they an artefact of the detector or the image display program?
Re: [ccp4bb] Strange spots
Kris, the link works for me and obviously for other people. I don't know why you don't have access to it... Anyway, thank you Konstantin for providing the pdf! Julian On 10/29/10 4:17 PM, Konstantin v. Korotkov wrote: The link worked for me, pages 320-322 attached. -Konstantin On Fri, 29 Oct 2010, Gerard Bricogne wrote: Dear Liz, You will be disappointed. I went immediately to that link, but page 321 is not available as part of the Googlebook sample, which jumps directly from page 320 to page 325. With best wishes, Gerard. -- On Fri, Oct 29, 2010 at 09:13:27PM +0100, elizabeth.d...@diamond.ac.uk wrote: There is always hope!!! Seriously though, I have never seen anything like this before! I am watching this thread with interest to see what others suggest. THanks Also thanks should go specifically to Julian Nomme who took the trouble to send us all the Helliwell book link. Liz From: CCP4 bulletin board on behalf of Sanishvili, Ruslan Sent: Fri 29/10/2010 21:08 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots C'mon now! Everybody knows that frogs in real space become handsome princes in the reciprocal one... N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Jacob Keller Sent: Friday, October 29, 2010 3:00 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots Yes, but the question is what in real space gives rise to reciprocal-space frog spawn? (Frogs, I guess?) - Original Message - From: Marcus Winter mailto:marcus.win...@agilent.com To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, October 29, 2010 2:56 PM Subject: Re: [ccp4bb] Strange spots Dear David, Further to the previous learned responses, surely, this is just frog spawn ? My apologies: it is a Friday evening, after all... Marcus Winter. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of David Goldstone Sent: 29 October 2010 17:08 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Strange spots Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgeway Mill Hill London NW7 1AA *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** -- Konstantin Korotkov, Ph.D. Research Scientist University of Washington Department of Biochemistry Box 357742 Seattle, WA 98195-7742 (206)616-4512 k...@u.washington.edu --
Re: [ccp4bb] Strange spots
The shape reminds me of the focused beam spot profile from slightly misaligned capillary optics. I don't have too much experience with these, but the incident beam profile does tend to propagate through to the spots on the detector. I wonder, could what you are seeing be a halo of minor incident beams, all converging on the sample, but at very different angles from the main beam. what you would see then is a circle of diffraction patterns around the usual pattern, but each at effectively a different crystal orientation (because the halo beams come in at different angles). This would explain why the effect only seems to be apparent for spots that are close to (but not at) the Bragg condition. What kind of x-ray setup is this? -James Holton MAD Scientist On 10/29/2010 9:08 AM, David Goldstone wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave
Re: [ccp4bb] Strange spots
They remind me of the fiber bundle on optic taper between the phosphor and the CCD. That's from things I saw years ago (BC - before crystallography) and I don't know the system in use here. I suspect it's instrumental and any diffraction in that area of the detector should show similar effects if there is a reflection there. Have you checked more images? This also gave me a great excuse to break out my newly arrived Atlas of Optical Transforms (thanks A.) and look at some more exotic explanations :) $5 from Amazon. Consider a spherical crystal :) Cheers, Eddie. From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of James Holton Sent: Friday, October 29, 2010 7:04 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Strange spots The shape reminds me of the focused beam spot profile from slightly misaligned capillary optics. I don't have too much experience with these, but the incident beam profile does tend to propagate through to the spots on the detector. I wonder, could what you are seeing be a halo of minor incident beams, all converging on the sample, but at very different angles from the main beam. what you would see then is a circle of diffraction patterns around the usual pattern, but each at effectively a different crystal orientation (because the halo beams come in at different angles). This would explain why the effect only seems to be apparent for spots that are close to (but not at) the Bragg condition. What kind of x-ray setup is this? -James Holton MAD Scientist On 10/29/2010 9:08 AM, David Goldstone wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave
