Re: [ccp4bb] Fwd: [ccp4bb] Wyckoff positions and protein atoms
On 16/12/2010 12:24, Ian Tickle wrote: I think this is how the Oxford CRYSTALS software ( http://www.xtl.ox.ac.uk/crystals.html ), which has been around for at least 30 years, deals with this issue, so I can't accept that it can't be made to work, even if I haven't got all the precise details straight of how it's done in practice. PS just to point out that CRYSTALS is now (since 2009) open source, so anyone can download it and find out for themselves how it's done! Do you have a link? I was looking and didn't find it Thanks Jon
Re: [ccp4bb] Fo-Fo Difference Map
Ian Tickle replied: (freezing soaking can easily induce 1% and sometimes 5% change), is surely the reason that Fo-Fo maps never caught on! I've been curious about this unit cell constant mis-matching for a while. If I understood well, Perutz tried to exploit the effect for phasing prior to heavy atom methods. As the unit cell changes, the diffraction peaks move, intensities change, and the fourier transform of the molecule is sampled in between the Bragg peaks. Has anyone tried to persue the idea since then? Cheers, Jon See, eg, Bragg Perutz, Proc. R. Soc. Lond. A 22 July 1952 vol. 213 no. 1115 425-435. doi: 10.1098/rspa.1952.0136
Re: [ccp4bb] Computer hardware and OS survey
Link,Todd M wrote: ... I did not find an equal web support page for Windows. It just isn't needed. If there is a windows version of a program you get to download, install, run and then get on with your life. Jon
Re: [ccp4bb] How small is a microbeam?
Sanishvili, Ruslan wrote: .. Reasons for discriminating 5-10 micron beams (minibeam) from ca 1 micron (microbeam) might have been not so much their size but what it involved to achieve these sizes. Might I ask - do you really get data from 1 micron protein crystals? The reduction in scattering power (==crystal volume) from 5x5x5 microns to 1x1x1 is 125 and so it seems to present a grand challenge. I had understood there to be a more fundamental size limit, coming from radiation damage, which is still several microns for typical proteins. Do you suggest that ~1 micron sized crystals are no longer exclusively in the domain of powder diffraction? Millions of crystals working together to increase the signal does help a lot for such tiny ones :-) Going back to the original question, with 'nano' instead of 'micro', the FDA has defined [1] a 100 nm size-range limit of nanotechnology. Name suggetions for 100nm - 999 nm are most welcome. Are they submicron? Cheers, Jon [1] http://www.fda.gov/nanotechnology/regulation.html
Re: [ccp4bb] Reindexing Orthorhombic
James Stroud wrote: ... What is the operation to reindex such that real space is rotated 180 about z? These are in P212121. Isn't that the 21 along z in your orthorhomic space group? Just apply it to your MR solution instead, and add an affine normaliser if needed to superpose the solutions. 'emma' in cctbx may help. Jon
Re: [ccp4bb] Looking for a free program for calculating powder diffraction pattern
Dear Owen, The GSAS package can do that: http://www.ccp14.ac.uk/solution/gsas/ It is important to put some values for the solvent contribution if you want to get a meaningful pattern. Shout if you need a hand. Good luck, Jon wob wrote: Hi, I'm looking for a free program for calculating powder diffraction pattern, given a PDB file. I googled for hours and only found a bunch of junks... Thanks for your help! Owen
Re: [ccp4bb] truncate ignorance
Borhani, David wrote: ... but I think pretty much everyone has converged on using it for the past many years. Many small molecule crystallographers seem to refine on intensity and so avoid need this procedure. Towards the end of the recent thread Wilson plot from truncated.mtz it had seemed like this forum was starting to see that light? In short - if your observations are supposed to be noisy in the plus_or_minus sigma sense then the peaks which are much less than the sigma should come out negative almost half of the time. Truncate would appear to be for the case where you want an estimate of the true magnitude of the structure factor, F, and not your experimental data. Jon
Re: [ccp4bb] Optimization of needle crystals?
You may be able to check whether the cyrstals are protein or detergent this using powder diffraction. (please excuse the shameless plug): Acta Cryst. (2008). A64, 169-180 Powder crystallography on macromolecules I. Margiolaki and J. P. Wright http://journals.iucr.org/a/issues/2008/01/00/sc5011/index.html Good luck, Jon Hubing Lou wrote: You didn't mention which detergent in the conditions. From the picture it looks like crystals of detergent. Quoting Ngo Duc Tri [EMAIL PROTECTED]: Dear ccp4 users, I crystallized a membrane protein and got some conditions showing the small needle crystals. All condition contained Mg2+ and high buffer pH. I learn that it is difficult to optimize the needle crystal. However I would like to ask your experience how to optimize in this case. Here is the attached picture of my crystal. Thank you very much for your advices! My best regards, TriNgo PhD Student - Sungkyunkwan University, Korea
Re: [ccp4bb] an over refined structure
Dear Ed, I don't see how you decouple symmetry mates in the case of a wrong space group. Symmetry mates should agree with each other typically within R_sym or R_merge percent, eg; about 2-5% . Observed and calculated reflections agree within R_Factor of each other, so about 20-30%. The experimental errors are pretty much negligible and overfitting is not a question about error bars; it is about how hard to push a round peg into a square hole? Cheers, Jon Edward Berry wrote: Actually the bottom lines below were my argument in the case that you DO apply strict NCS (although the argument runs into some questionable points if you follow it out). In the case that you DO NOT apply NCS, there is a second decoupling mechanism: Not only the error in Fo may be opposite for the two reflections, but also the change in Fc upon applying a non-symmetrical modification to the structure is likely to be opposite. So there is no way of predicting whether |Fo-Fc| will move in the same direction for the two reflections. I completely agree with Dirk (although I am willing to listen to anyone explain why I am wrong). Ed Edward Berry wrote: Dean Madden wrote: Hi Dirk, I disagree with your final sentence. Even if you don't apply NCS restraints/constraints during refinement, there is a serious risk of NCS contaminating your Rfree. Consider the limiting case in which the NCS is produced simply by working in an artificially low symmetry space-group (e.g. P1, when the true symmetry is P2): in this case, putting one symmetry mate in the Rfree set, and one in the Rwork set will guarantee that Rfree tracks Rwork. I don't think this is right- remember Rfree is not just based on Fc but Fo-Fc. Working in your lower symmetry space group you will have separate values for the Fo at the two ncs-related reflections. Each observation will have its own random error, and like as not the error will be in the opposite direction for the two reflections. Hence a structural modification that improves Fo-Fc at one reflection is equally likely to improve or worsen the fit at the related reflection. The only way they are coupled is through the basic tenet of R-free: If it makes the structure better, it is likely to improve the fit at all reflections. For sure R-free will go down when you apply NCS- but this is because you drastically improve your data/parameters ratio. Best, Ed
Re: [ccp4bb] To bathe or not to bathe.
It'd be interesting to determine the validity of the assumption that absorption is simply a function of frame number. ... and direction. See, eg: Acta Cryst. (1995). A51, 33-38[ doi:10.1107/S0108767394005726 ] An empirical correction for absorption anisotropy R. H. Blessing Best, Jon
Re: [ccp4bb] The importance of USING our validation tools
Think this bounced last time I tried to mail it in, a simulator exists at: http://fable.sourceforge.net/index.php/Farfield_Simulation Jon Eleanor Dodson wrote: ZO has a good point - it is a pain trying to get decent simulated material - maybe there is an employment opportunity here? Eleanor Zbyszek Otwinowski wrote: James Holton wrote: How MUCH do you want to bet? ;) Any amount, as long as we are taking about real diffraction images corresponding to the deposited file with observed structure factors. I doubt that simulated diffraction images will be shown, because they are easy to be recognized as such. Independently, I value the possibility of data simulation in methods development and for teaching purposes. Zbyszek Otwinowski UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, TX 75390-8816 (214) 645 6385 (phone) (214) 645 6353 (fax) [EMAIL PROTECTED]
Re: [ccp4bb] Is anomalous signal a different wavelength?
James, At least for diffraction experiments; the photon scatters off of the *crystal lattice*, not any individual electron, so you can conserve the momentum of the photons and the macroscopic crystal without the crystal recoiling too much. Best, Jon Murray, James W wrote: Dear All, While we are talking about X-ray scattering, I have another question. If an X-ray is elastically scattered from an electron at an angle theta, its energy is the same is the incoming X-ray. However, the momentum is not the same, as it now has a component in a perpendicular direction (see fig below). As I don't believe that the conservation of momentum really is violated, what is the source of the discrepancy? Contrast this with most textbook descriptions of Compton scattering, where the X-ray loses energy and the electron gains kinetic energy. best wishes James X-ray e- \ \ \ Dr. James Murray Biochemistry Building Department of Biological Sciences Imperial College London London, SW7 2AZ Tel: +44 (0)20 7594 5276
[ccp4bb] Announcement: Workshop on Powder Diffraction with Proteins
Workshop on the Development and Direction of Powder Diffraction on Proteins ESRF, Grenoble, France, 22-23 June 2007 http://www.esrf.fr/events/conferences/PowderDiffraction The investigation of protein structures by high-resolution powder X-ray diffraction has been established as a complementary tool to recognized single-crystal techniques. When suitable crystals are not available, a micro-crystalline powder can give at least basic information about the crystal lattice, symmetry and crystallinity. Recently it has been demonstrated that structure solution of small proteins can be successful using powder data via traditional and/or novel approaches. The 2-day workshop will cover topics such as sample preparation, data-collection, strategies for data analysis, structure validation, etc. for powder material including proteins. We are aiming for a constructive meeting with powder diffraction experts, structural and molecular biologists, colleagues from the pharmaceutical industry and software developers participating. The meeting will be hosted by the ESRF in Grenoble, France and will take place on the 22d and 23d of June 2007 following the EMBO07 practical course. The number of participants is limited to 50 and application is open till May 30th, 2007. Further information can be found in our web pages http://www.esrf.fr/events/conferences/PowderDiffraction.
Re: [ccp4bb] Advice on img proc software
The mathcad image processing module is too expensive for my taste. My university has a campus- wide license for Matlab, so it's *free* for me... I have no idea of what it would cost to purchase. [reminder: never compare educational licensing with giving drugs to schoolchildren.] For something similar to matlab it might be worth investigating python+matplotlib, which are free for everyone (http://www.scipy.org/NumPyProConPage). The script below does a phase/amplitude swap using an fft that came with the old Numeric package, nowadays it might have a different name and hiding place. Best, Jon --- from matplotlib.pylab import * import FFT # test data: i = reshape(array(range(256)*256) , (256,256) ) j = transpose(i) circle = where( (i-128)*(i-128) + (j-128)*(j-128) 3000 , 10. , 0) square = where( abs(i-128) + abs(j-128) sqrt(2500) , 10. , 0) # transform image1 = circle image2 = square ft1 = FFT.fft2d(image1) ft2 = FFT.fft2d(image2) phi1=arctan2(ft1.real , ft1.imag) phi2=arctan2(ft2.real , ft2.imag) amp1phi2 = FFT.inverse_fft2d(abs(ft1)*sin(phi2) + abs(ft1)*cos(phi2)*1j) amp2phi1 = FFT.inverse_fft2d(abs(ft2)*sin(phi1) + abs(ft2)*cos(phi1)*1j) # plots: subplot(221);title(image1);imshow(image1) subplot(222);title(image2);imshow(image2) subplot(223);title(amp1 phi2);imshow(amp1phi2) subplot(224);title(amp2 phi1);imshow(amp2phi1) show()
Re: [ccp4bb] crytstallographic software
Kevin Cowtan wrote: Acta D has for some reason a rather poor impact rating, and J. Appl. Cryst. a rather better one. There is no outlier rejection in the calculations for journal citation reports (eg: impact factors). Congratulations to: Spek AL, Single-crystal structure validation with the program PLATON, J. Appl. Cryst 2003, 36, 7. This one paper collected 985 citations in 2005, over half of the 1768 citations for the journal in that year. It is too old to be counted in the next round, and Acta D is likely to improve again following the creation of Acta F in 2005. -Jon
