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Re: [ccp4bb] Refining against images instead of only reflections |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: Refining against images instead of only reflections From: Klaus_Fütterer k {- dot -} futterer {- at -} BHAM {- dot -} AC {- dot -} UK Date: 2010-01-20 A long time ago I did a bit of Rietveld refinement and I see some similarities between this approach and what people have been proposing in this thread. Refining against the profile of the 1-d powder diffraction pattern rather than extracting integrated intensities helped to improve the quality of the refined structures significantly. Finding the correct (or best) profile function, however, took a while, at least for the X-ray case. Klaus ======================================================================= Klaus Fütterer, Ph.D. Reader in Structural Biology School of Biosciences P: +44-(0)-121-414 5895 University of Birmingham F: +44-(0)-121-414 5925 Edgbaston E: k.futterer@bham.ac.uk Birmingham, B15 2TT, UK W: www.biochemistry.bham.ac.uk/klaus/ ======================================================================= On 20 Jan 2010, at 20:29, Edward Snell wrote: > Hi Paul, > > I'll probably open myself up to criticism (welcomed) but I think > I'd disagree with this somewhat. While crystallography from the > Bragg reflections provides a nice static picture of the structure, > looking at the diffuse scatter in more detail may give more > knowledge about mechanism - i.e. if there are any characteristic > modes associated with significant motion etc. Higher resolution is > not always good, one of my enlightening experiences came from > paying attention to collecting very complete, very low resolution > data. Similarly, after collecting 0.8A data from a large protein I > leant a lot about data processing but even more about how to not > tell anyone, move the detector back, and then attenuate the beam :) > The high-res provided a lot more work and didn't provide any more > useful structural knowledge than a 1.2A data set collected in a > fraction of the time. However, it did provide a window into how X- > rays can perturb the structure - being greedy is not always good. > > Diffuse scattering has been neglected in the field (for good > reason) but I think we have the processing power to take advantage > of it now. To misquote Richard Feynman, "there is plenty of room at > the bottom", make sure you get the low resolution information as > well as the high. > > I do agree that we may have to rethink image storage somewhat. > Looking over a paper not too long ago that had over 30,000 images > involved in the analysis made me remember the days when the tape > drives were slower writing data than the detectors producing it. > That mad scramble to start backup before starting collection ;) > Realtime readout, continuous rotation etc., may need to redefine > our thoughts of images. > > Cheers, > > Eddie > > Edward Snell Ph.D. > Assistant Prof. Department of Structural Biology, SUNY Buffalo, > Hauptman-Woodward Medical Research Institute > 700 Ellicott Street, Buffalo, NY 14203-1102 > Phone: (716) 898 8631 Fax: (716) 898 8660 > Skype: eddie.snell Email: esnell@hwi.buffalo.edu > Telepathy: 42.2 GHz > > Heisenberg was probably here! > > > -----Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf > Of Paul Smith > Sent: Wednesday, January 20, 2010 3:00 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Refining against images instead of only > reflections > > Hi Jacob, > > I see you're still in the crystallography business. > > While you have an interesting idea, I doubt refining structures > against entire images would be of any use in obtaining higher > quality macromolecular structures. Much of what you see on the > screen is a function of parameters completely unrelated or > irrelevant to the structure being studied. Diffuse scattering can > come from the cryo liquid surrounding the crystal as well as the > fibers of the mounting loop itself. Background scattering is > related to beam collimation. Spot size/shape is a function of > crystal morphology among other things. In addition, every detector > has its own peculiarities that make the intensities observed apart > from diffraction spots particular to that detector. Also, you > would have to take into account other physical properties such as > ambient temperature, detector dark current fluctuations, variations > in air absorption, etc. > > So, you could conceivably fit all of these various parameters to > the images on hand, but none of them give you any actual > information about your structure. As always, if you want more > information about your structure, get higher resolution data. > > Nonetheless, I do think some thought could be put in to exactly how > data are reduced. Perhaps the impending era of real time detector > readout will help us rethink about spot profiles and intensity > integration in a more sophisticated way. We may see a return to > thinking about ccd readouts like an area detector which makes the > process of analyzing images moot. > > --Paul > > --- On Wed, 1/20/10, Jacob Keller > wrote: > >> From: Jacob Keller >> Subject: [ccp4bb] Refining against images instead of only reflections >> To: CCP4BB@JISCMAIL.AC.UK >> Date: Wednesday, January 20, 2010, 12:47 PM >> Dear Crystallographers, >> >> One can see from many posts on this listserve that in any >> given x-ray diffraction experiment, there are more data than >> merely the diffraction spots. Given that we now have vastly >> increased computational power and data storage capability, >> does it make sense to think about changing the paradigm for >> model refinements? Do we need to "reduce" data anymore? One >> could imagine applying various functions to model the >> intensity observed at every single pixel on the detector. >> This might be unneccesary in many cases, but in some cases, >> in which there is a lot of diffuse scattering or other >> phenomena, perhaps modelling all of the pixels would really >> be more true to the underlying phenomena? Further, it might >> be that the gap in R values between high- and low-resolution >> structures would be narrowed significantly, because we would >> be able to model the data, i.e., reproduce the images from >> the models, equally well for all cases. More information >> about the nature of the underlying macromolecules might >> really be gleaned this way. Has this been discussed yet? >> >> Regards, >> >> Jacob Keller >> >> ******************************************* >> 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-keller2@northwestern.edu >> ******************************************* >> CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999 |
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