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
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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: [log in to unmask]
Birmingham, B15 2TT, UK W: www.biochemistry.bham.ac.uk/klaus/
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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: [log in to unmask]
> Telepathy: 42.2 GHz
>
> Heisenberg was probably here!
>
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf
> Of Paul Smith
> Sent: Wednesday, January 20, 2010 3:00 PM
> To: [log in to unmask]
> 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 <[log in to unmask]>
> wrote:
>
>> From: Jacob Keller <[log in to unmask]>
>> Subject: [ccp4bb] Refining against images instead of only reflections
>> To: [log in to unmask]
>> 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: [log in to unmask]
>> *******************************************
>>
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