Hi
I, too, was struck by the potential similarity with Rietveld
refinement, then started to think about the differences. The biggest
difference, of course, is refining against "many" two-dimensional
images compared to refining against a linear plot - so I'd guess in
principle you'd get a big benefit in increasing the data:parameter
ratio.
Of course, there's a hint above in the "refinement" part of the
process; you need the structure and a model for the causes of the
diffuse scatter etc to have something to refine against, so it may
still be worthwhile extracting the Bragg intensities first to solve
your structure.
(I've never done Rietveld refinement, but read a good book on the
topic a few years ago - "The Riteveld Method" ed R.A. Young. It might
be a little out of date now...)
On 20 Jan 2010, at 21:14, Klaus Fütterer wrote:
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.futte...@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: 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
*******************************************
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre,
Hills Road, Cambridge, CB2 0QH
