Hi James I think the answer to your question about the 'R-factor gap' is easy to answer (but not so easy to solve!). It's obviously due to the inadequacy of our models, particularly with regards to thermal motion (anisotropy, anharmonicity etc), disorder & motion correlation/diffuse scatter, also bonding effects, none of which you have included in your simulation (yes I know you said you included diffuse scatter but I guess it's only the basic isotropic 'Einstein model', not the more realistic models of acoustic/optic scattering taking into account motion correlation between different atom densities). Granted most of these (with the obvious exception of anisotropy and possibly bonding effects) are not included in small molecule models either, which would lead one to conclude that the remaining effects of anharmonicity, motion correlation and disorder are much more severe in a protein crystal.
Having said all that, I think it's a great idea to have the capability to generate fake data, and the more realistic it is the better! It's so much easier debugging programs when you know the right answer! Cheers -- Ian > -----Original Message----- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of James Holton > Sent: 20 March 2009 12:29 > To: CCP4BB@jiscmail.ac.uk > Subject: fake images > > 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 Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). 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