There was a thread a while back which related to this a bit:
"Re: [ccp4bb] Small lines in diffraction pattern (more info)"
In that thread, there were mentioned the papers:
Faure et al NSB 2 Feb 1994
Kajiwara J. Appl. Cryst. (1971). 4, 329
These seem to bear on the issue of diffuse scattering, and in particular the
procedure in the NSB paper could in principle be applied to model
refinements, I think.
Jacob
*******************************************
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
*******************************************
----- Original Message -----
From: "Edward Snell" <esn...@hwi.buffalo.edu>
To: <CCP4BB@JISCMAIL.AC.UK>
Sent: Wednesday, January 20, 2010 2:29 PM
Subject: Re: [ccp4bb] Refining against images instead of only reflections
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: esn...@hwi.buffalo.edu
Telepathy: 42.2 GHz
Heisenberg was probably here!
-----Original Message-----
From: CCP4 bulletin board [mailto:ccp...@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 <j-kell...@md.northwestern.edu> wrote:
From: Jacob Keller <j-kell...@md.northwestern.edu>
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-kell...@northwestern.edu
*******************************************
