Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
On 11/02/2010 02:36 PM, Buz Barstow wrote: Dear All, I'm looking for a software program to produce, given a 3D atomic structure of a molecule, a linear map showing the surface accessibility of residues in a protein structure. Would any one know of a program that can produce this sort of map. Thanks! and all the best, --Buz Have you looked at the PISA output - that lists all such information residue by residue? Eleanor
[ccp4bb] ***Reminder*** Biological Structures Group BCA Winter Meeting - Wed 15th December, University of Reading - DON'T FORGET TO REGISTRATION TODAY!
*REMINDER** Biological Structures Group BCA Winter Meeting Wednesday 15th December 2010 University of Reading Hosted by the School of Biological Sciences *** Registration details can be found at: http://www.reading.ac.uk/biologicalsciences/businessdevelopment/biosci-BCAwi ntermeet.aspx Thank you!
Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
Dear All, Thanks for your suggestions! I ended up using the areaimol program in ccp4. My next question: Given a list of accessible surface area, is there a generally accepted value of ASA above which a residue classifies as a surface residue, while below this number it is an interior residue? Thanks! and all the best, --Buz On Nov 2, 2010, at 10:56 AM, Tim Gruene wrote: > Hello Buz, > > I do not know what you mean by 'linear map', but according to its manual, the > ccp4-program "surface" writes a list of accessible are per atom per residue, > which you could convert into the total fraction per residue with not too much > effort. > > Is this what you are looking for? > > Cheers, Tim > > On Tue, Nov 02, 2010 at 10:36:56AM -0400, Buz Barstow wrote: >> Dear All, >> >> I'm looking for a software program to produce, given a 3D atomic structure >> of a molecule, a linear map showing the surface accessibility of residues in >> a protein structure. >> >> Would any one know of a program that can produce this sort of map. >> >> Thanks! and all the best, >> >> --Buz > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > phone: +49 (0)551 39 22149 > > GPG Key ID = A46BEE1A >
Re: [ccp4bb] SUMMARY: finding from HKL Scalepack
Thanks very much for all of the helpful suggestions! The most useful solution for us was a python script provided by Ed Pozharski at the ccp4wiki link below, which reads a .sca file and produces a table with both and / for a user-defined number of shells. http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Calculate_av erage_I/sigma_from_.sca_file Other suggestions are listed below: >From Ed Pozharski: ctruncate outputs the table with Mn(F/sd) (which will be twice Mn(I/sd)) when it does anisotropy analysis >From Phil Jeffrey: I personally report but wrote my own program to do it from the .sca files. >From Paul Smith: I have a perl utility that does much of what you would like. It will run scalepack for you iteratively until the number of rejections converges, or it will parse scalepack output. The output has by shell gleaned from the scale log with the same resolution bins used in scaling. The usage for parsing is "autoscale.pl -e scale.log" >From Wladek Minor: Click report on the top panel and you will get all relevant statistics that are necessary for publications. >From Graeme Winter: You can still get this analysis with Scala even after scaling with scalepack. If you output the measurements unmerged (no merge original index) you can convert them to MTZ using pointless, then remerge the data as follows: scala hkiin from_pointless.mtz hklout merged.mtz << eof run 1 all scales constant sdcorrection noadjust norefine both 1 0 0 cycles 0 eof (pointless -c scain ... - you will also need to assign the cell and symmetry) This will just remerge the measurements and give you the usual merging analysis from Scala. Very useful. Same trick also works with data from XDS/XSCALE. From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Radisky, Evette S., Ph.D. Sent: Monday, November 01, 2010 4:18 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] finding from HKL Scalepack Dear all, I have previously used SCALA for data reduction, and in publications and pdb depositions, reported the "Mn(I/sd)" output from SCALA for the whole data set and for the highest resolution shell. We now have some data that has instead been reduced using the HKL suite, and I am confused about how to find the value that would be equivalent to Mn(I/sd) from SCALA. For I/Sigma(I) I've been advised by a colleague more familiar with HKL to manually calculate from average I divided by average error (sigma). As pointed out in a previous ccp4bb thread, this would give me /, which is not the same as . Two questions: (1) Is this / what is generally reported in the literature for data processed with the HKL suite? (2) Since I would also like to know the Mn(I/sd) by shell anyway so that I can compare to previous data sets, is there a way to extract this value from the scalepack log, or is there a simple reflection file analysis utility that could read the .sca or .mtz file to extract this information? Thanks for any clarifications or suggestions! Evette Evette S. Radisky, Ph.D. Assistant Professor Mayo Clinic Cancer Center Griffin Cancer Research Building, Rm 310 4500 San Pablo Road Jacksonville, FL 32224 (904) 953-6372
Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
That depends on what you are trying to do. Maybe the best strategy is to use fuzzy logic, whereby a residue which has 30% of it's Gly-X-Gly ASA buried has the "surfaceness" of 0.7. On Wed, 2010-11-03 at 09:55 -0400, Buz Barstow wrote: > Dear All, > > Thanks for your suggestions! I ended up using the areaimol program in ccp4. > > My next question: > > Given a list of accessible surface area, is there a generally accepted value > of ASA above which a residue classifies as a surface residue, while below > this number it is an interior residue? > > Thanks! and all the best, > > --Buz > > > On Nov 2, 2010, at 10:56 AM, Tim Gruene wrote: > > > Hello Buz, > > > > I do not know what you mean by 'linear map', but according to its manual, > > the > > ccp4-program "surface" writes a list of accessible are per atom per residue, > > which you could convert into the total fraction per residue with not too > > much > > effort. > > > > Is this what you are looking for? > > > > Cheers, Tim > > > > On Tue, Nov 02, 2010 at 10:36:56AM -0400, Buz Barstow wrote: > >> Dear All, > >> > >> I'm looking for a software program to produce, given a 3D atomic structure > >> of a molecule, a linear map showing the surface accessibility of residues > >> in a protein structure. > >> > >> Would any one know of a program that can produce this sort of map. > >> > >> Thanks! and all the best, > >> > >> --Buz > > > > -- > > -- > > Tim Gruene > > Institut fuer anorganische Chemie > > Tammannstr. 4 > > D-37077 Goettingen > > > > phone: +49 (0)551 39 22149 > > > > GPG Key ID = A46BEE1A > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
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 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
[ccp4bb] limit for number of files for CAD...
CCP4'ers, Are 9 datasets the maximum for an mtz file? or a single run of cad? The manual (http://www.ccp4.ac.uk/html/cad.html) seems to suggest that 9 is the limit per cad run but not for a given mtz. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] limit for number of files for CAD...
Hello, 9 mtz files are the limit of CAD, one things you can do is to modify the source file , that is wrote in fortran, or write a bash script or that run iteratively the CAD script and change the MTZ files. R. On 03/11/2010 18:11, Francis E Reyes wrote: CCP4'ers, Are 9 datasets the maximum for an mtz file? or a single run of cad? The manual (http://www.ccp4.ac.uk/html/cad.html) seems to suggest that 9 is the limit per cad run but not for a given mtz. F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D -- @ @ @ Rita Giordano @ @ Structural Biology Group, ESRF @ @ Grenoble France@ @ http://www.esrf.fr @ @ E-mail: rita.giord...@esrf.fr @ @ @
Re: [ccp4bb] limit for number of files for CAD...
Hi Francis, the limit ist for CAD. You can put as much datasets as you want in one mtz, but you have to run cad than stepwise. Be careful with the column labels. Duplicate labels lead to problems. Christian Am Mittwoch 03 November 2010 18:11:34 schrieb Francis E Reyes: > CCP4'ers, > > Are 9 datasets the maximum for an mtz file? or a single run of cad? > The manual (http://www.ccp4.ac.uk/html/cad.html) seems to suggest that > 9 is the limit per cad run but not for a given mtz. > > F > > > > - > Francis E. Reyes M.Sc. > 215 UCB > University of Colorado at Boulder > > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D > > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D >
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" To: 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] limit for number of files for CAD...
Yes, CAD is limited to 9 input files. I seem to remember I once tried to increase the limit, but got into problems (it is not just a case of increasing MAXFILES). It is far simpler and safer to run CAD iteratively. But an MTZ file can hold more. The current limits are: #define MXTALS 100 #define MSETS 1000 #define MCOLUMNS 1 In principle, we could remove these limits, but I guess they are ok in most normal cases ... m On Wed, 2010-11-03 at 18:20 +0100, Rita GIORDANO wrote: > Hello, > 9 mtz files are the limit of CAD, one things you can do is to modify the > source file , that is wrote in fortran, or write a bash script or that > run iteratively the CAD script and change the MTZ files. > > R. > > On 03/11/2010 18:11, Francis E Reyes wrote: > > CCP4'ers, > > > > Are 9 datasets the maximum for an mtz file? or a single run of cad? The > > manual (http://www.ccp4.ac.uk/html/cad.html) seems to suggest that 9 is > > the limit per cad run but not for a given mtz. > > > > F > > > > > > > > - > > Francis E. Reyes M.Sc. > > 215 UCB > > University of Colorado at Boulder > > > > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D > > > > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D > -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603634Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
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 > 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] limit for number of files for CAD...
I have a version which I modified a while back to handle up to 999 files simultaneously, and which I can send to anyone privately on request, as long as you accept the entire risk of using it (and you should probably also heed Martyn's warning!). It has probably diverged from the distributed version and may not have benefitted from any recent (and no-so-recent) bugfixes, so no guarantees to fix it if it doesn't work for you! And yes it was a pig to get it working, it wasn't just a matter of increasing MAXFILES, the file limits are also embedded in the labels. Caveat emptor! Cheers -- Ian On Wed, Nov 3, 2010 at 5:34 PM, Martyn Winn wrote: > Yes, CAD is limited to 9 input files. I seem to remember I once tried to > increase the limit, but got into problems (it is not just a case of > increasing MAXFILES). It is far simpler and safer to run CAD > iteratively. > > But an MTZ file can hold more. The current limits are: > #define MXTALS 100 > #define MSETS 1000 > #define MCOLUMNS 1 > > In principle, we could remove these limits, but I guess they are ok in > most normal cases ... > > m > > > On Wed, 2010-11-03 at 18:20 +0100, Rita GIORDANO wrote: >> Hello, >> 9 mtz files are the limit of CAD, one things you can do is to modify the >> source file , that is wrote in fortran, or write a bash script or that >> run iteratively the CAD script and change the MTZ files. >> >> R. >> >> On 03/11/2010 18:11, Francis E Reyes wrote: >> > CCP4'ers, >> > >> > Are 9 datasets the maximum for an mtz file? or a single run of cad? The >> > manual (http://www.ccp4.ac.uk/html/cad.html) seems to suggest that 9 is >> > the limit per cad run but not for a given mtz. >> > >> > F >> > >> > >> > >> > - >> > Francis E. Reyes M.Sc. >> > 215 UCB >> > University of Colorado at Boulder >> > >> > gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D >> > >> > 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D >> > > -- > *** > * * > * Dr. Martyn Winn * > * * > * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * > * Tel: +44 1925 603455 E-mail: martyn.w...@stfc.ac.uk * > * Fax: +44 1925 603634 Skype name: martyn.winn * > * URL: http://www.ccp4.ac.uk/martyn/ * > *** >
Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues
Hi Buz, Sorry to respond a little late, but if you are still tinkering with surface accessibility calculations, you can use the following web server that will calculate the "diffusion accessibility" of each atom in your input .pdb file: http://nihserver.mbi.ucla.edu/diff_acc/ "Diffusion accessibility" is slightly different from "surface accessibility," so depending on what you're interested in this may not be exactly what you want. From the web server: "Diffusion accessibility gives a measure of surface accessibility that is longer range in nature than ordinary solvent accessibility. The idea of diffusion accessibility was introduced several years ago (Yeates, TO (1995) Algorithms for Evaluating the Long-range Accessibility of Protein Surfaces. J Mol Biol 249(4): 804-15). Diffusion accessibility is a measure of how easily or frequently a specific point on a surface would capture a hypothetical diffusing (or randomly-walking) probe that is captured upon its first encounter with any part of a surface. Naturally, parts of a surface that are solvent-exposed in the traditional sense but lie in a deep surface depression will capture the probe only rarely, since the probe will more often encounter another part of the surface first. The results of a diffusion accessibility calculation can be useful in quantitatively evaluating potential binding regions of a protein surface, and are particularly useful in visualization." The reason I still mention this is because diffusion accessibility vs. surface accessibility may be one way to answer your question of how to identify a surface residue vs. an interior residue. Also, the web server will output another .pdb file with the diffusion accessibility for each atom rewritten into the B-factor column. This is particularly useful for visualizing the "surfaceness" (as Ed put it) of each atom because you can open the output coordinates in PyMol and color atoms by B-factor which will give you a nice, colorful representation of the accessibility of the surface. Hope this is helpful, Mike - Original Message - From: "Buz Barstow" To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, November 3, 2010 6:55:54 AM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] Software to Produce Linear Map of Surface Accessible Residues Dear All, Thanks for your suggestions! I ended up using the areaimol program in ccp4. My next question: Given a list of accessible surface area, is there a generally accepted value of ASA above which a residue classifies as a surface residue, while below this number it is an interior residue? Thanks! and all the best, --Buz On Nov 2, 2010, at 10:56 AM, Tim Gruene wrote: > Hello Buz, > > I do not know what you mean by 'linear map', but according to its manual, the > ccp4-program "surface" writes a list of accessible are per atom per residue, > which you could convert into the total fraction per residue with not too much > effort. > > Is this what you are looking for? > > Cheers, Tim > > On Tue, Nov 02, 2010 at 10:36:56AM -0400, Buz Barstow wrote: >> Dear All, >> >> I'm looking for a software program to produce, given a 3D atomic structure >> of a molecule, a linear map showing the surface accessibility of residues in >> a protein structure. >> >> Would any one know of a program that can produce this sort of map. >> >> Thanks! and all the best, >> >> --Buz > > -- > -- > Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > phone: +49 (0)551 39 22149 > > GPG Key ID = A46BEE1A > -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
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" To: 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 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 *** <>
