Did anybody notice the serendipity of the "smeared spots" question just asked on the bb? I wonder whether, with the proposed new software, this data set could actually be used to solve a structure? In fact, these images look pretty similar to those in the NSB paper I cited previously.
Jacob Keller
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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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----- Original Message -----
From: John R Helliwell
To: [log in to unmask]
Sent: Thursday, January 21, 2010 3:49 AM
Subject: Re: [ccp4bb] Refining against images instead of only reflections
Dear Jacob,
Your approach I think it is a sound one for exploring how to gain a significant potential improvement by harnessing the diffuse diffraction, which looks rich and varied in many cases ie must surely contain good structural information. The separation of the various experimental and crystal (imperfection) features is a part of moving towards such a quantitative analysis.
The diffuse scattering interpretation past examples have involved modelling eg from subjectively obvious looking protein domains and hinge rotation possibilities for example. A more objective approach woulod be to combine the Bragg-derived-protein-structure with molecular dynamics (MD) simulations ie which may then explain in part the observed diffuse X-ray scattering, mainly but not exclusively between the Bragg peaks. Such MD simulations to my mind have improved a lot with the compute power readily available, either to extend the length of time of the simulations or initiate from multiple starting points (eg temperatures) to assess sensible time-evolutions of the structure.
On getting funded:- Falling between two funding Agencies is a universal challenge, not only USA. I cannot guarantee success but one approach here in UK is to contact both likely Agencies' relevant Programme Managers and initiate a three way e-discussion. After all they can contemplate sharing the cost!
Good luck,
Best wishes,
John
Prof John R Helliwell
On Wed, Jan 20, 2010 at 5:47 PM, Jacob Keller <[log in to unmask]> wrote:
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]
*******************************************
--
Professor John R Helliwell DSc
