Yes, Harry, indeed there is a program for simulating diffraction
patterns. You can get a development snapshot of it here:
http://bl831.als.lbl.gov/~jamesh/mlfsom/development_snapshot.tar.gz
MLFSOM (mosflm in reverse) is not the only program of its kind in
existence and I don't think it is a good idea to keep the fact that they
exist a secret in any way. In fact, MLFSOM has been extremely
instructive in establishing how important different sources of error are
to the structure determination process, and where the "threshold of
solvability" is in real-world units. I am writing this up now and I
have given several talks about it recently but it has always puzzled me
that noone has EVER asked me if there is some way to "identify as fake"
the images that come from MLFSOM. The answer to this question is: "Yes,
there are several".
Moving on...
When it comes to Garib's original question of "do we need the images", I
am definitely of the opinion that the answer to this question is "yes".
In fact, I would like to ask Garib and everyone else if they can answer
the question: Why is Rcryst/Rfree from almost every protein crystal
structure on the order of 20% when the intensities are generally
measured to better than 5%? What are we missing? Small molecule
structures are unpublishable with Rcryst > Rsym because this means that
the presented model does not explain the observations to within
experimental error. I will tell you for nothing that if you feed fake
data from MLFSOM into Elves and ARP/wARP, you will get back an
Rcryst/Rfree that is roughly equal to Rsym (~5-6%), so this means that
none of the sources of error I have included in MLFSOM: photon-counting
noise, shutter jitter, beam flicker, sample vibration, diffuse scatter,
absorption effects, funny spot shapes, radiation damage, detector
read-out and calibration noise. None of these sources of error are big
enough to explain the "R-factor gap" in macromolecular crystallography.
So, if you don't know what it is we are missing, how can you be sure it
is not in the image data?
-James Holton
MAD Scientist
harry powell wrote:
Hi
I've heard of a tool from the Golden State which could (potentially)
be used for forging diffraction images... I believe it's called "mlfsom".
On 18 Mar 2009, at 17:50, Felix Frolow wrote:
One convincing argument I have:
We will be able to catch fraud ultimately. Fraud is a devastation for
structural biology.
...Unless they will be smart enough to forge diffraction data images,
not a big deal.
The second one - in the case of a controversy of the deposited
results (possible thing) we can try to re-interpret the space group
and Bravais lattice
And one more, when we have time we can show that we know better to
process and to refine ;-)
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Biotechnology
Tel Aviv University 69978, Israel
Acta Crystallographica D, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972 3640 8723
Fax: ++972 3640 9407
Cellular: ++972 547 459 608
On Mar 18, 2009, at 6:41 PM, Garib Murshudov wrote:
Dear all
Before going into and trying to find a technical solution to the
problem it would be good if decide if we need images. As far as I
know if we face with a problem to solve and we know that it is
necessary to solve then we find technical solution to the problem
(either from other fields or we find our own solution with some
elements of reinvention of new MX wheels).
Do we need images to store? What kind of information we can extract
from images that we cannot from amplitudes, intensities (even
unmerged)? Does anybody have a convincing argument for favour of
images?
regards
Garib
On 18 Mar 2009, at 16:32, Herbert J. Bernstein wrote:
Actually the radiologists who manage CT and PET scans of brains do
have
a solution, called DICOM, see http://medical.nema.org/. If we work
together as a community we should be able to do as well as the
rocket scientists and the brain surgeons' radiologists, perhaps even
better. -- Herbert
=====================================================
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
+1-631-244-3035
y...@dowling.edu
=====================================================
On Wed, 18 Mar 2009, Jacob Keller wrote:
Apparently it DOES take a rocket scientist to solve this problem.
Maybe the brain surgeons also have a solution?
JPK
*******************************************
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: "Klaas Decanniere"
<klaas.decanni...@vub.ac.be>
To: <CCP4BB@JISCMAIL.AC.UK>
Sent: Wednesday, March 18, 2009 5:36 AM
Subject: Re: [ccp4bb] images
Herbert J. Bernstein wrote:
Other sciences have struggled with this and seem to have found an
answer.
Have e.g. a look at http://heasarc.nasa.gov/docs/heasarc/fits.html
kind regards,
Klaas
This is a good time to start a major crystallogrpahic image
archiving effort. Money may well be available now that will not be
avialable six month from now, and we have good, if not perfect,
solutions available for many, if not all, of the technical issues
involved. Is it really wise to let this opportunity pass us by?
The deposition of images would be possible providing some
consistent
imagecif format was agreed.
This would of course be of great use to developers for certain
pathological cases, but not I suspect much value to the user
community - I down load structure factors all the time for test
purposes but I probably would not bother to go through the data
processing, and unless there were extensive notes associated with
each set of images I suspect it would be hard to reproduce
sensible
results.
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills
Road, Cambridge, CB2 0QH
