Felix I would be very surprised if anyone could calculate the expected Rfree in this case with any degree of reliability, since it seems to have been refined with a combination of TLS and rigid-bond/sphericity anisotropic ADP restraints. Taking account of restraints, particularly thermal ones which have to be assigned ad hoc weights in the absence of experimentally observed ones (as is the case with geometrical restraints) in the calculation of <Rfree> is non-trivial!
Cheers -- Ian > -----Original Message----- > From: owner-ccp...@jiscmail.ac.uk [mailto:owner-ccp...@jiscmail.ac.uk] On > Behalf Of Felix Frolow > Sent: 20 March 2009 14:31 > To: James Holton > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] fake images and R-Rfree values > > I must add something... > ID14-2 beam line in our hands produced during first decade of 2000's > data sets that > for structures at about 1.8 - 1.6 Angstrom constantly leaded to a very > good R - Rfree (in the range of 12 %-18%) > As an example see PDB entry 1Y9A. If will be needed I will supply > diffraction data for several structures. Such quality produces > problems as a referee > accused us by "over-fitting Rfree" whatever it means. He also "new" > what is a theoretical difference of R-Rfree in any resolution? > During our discussions recently with Dr Alexander Popov, responsible > for the ESRF ID23-1 beam line on this matter Dr Popov suggest that > it is > because the X-ray beam on this station is very large. I also think > that its is largely parallel, old quality of the synchrotron lines. > Maybe other people who noticed similar thing may add more. > > BTW final data set scaling statistics (SCALEPAK) is shown: > > Shell Lower Upper Average > Average Norm. > Linear Square > limit Angstrom I > error stat. Chi**2 R- > fac R-fac > > 20.00 3.79 7081.7 258.9 > 136.6 1.172 > 0.029 0.031 > 3.79 3.01 3894.0 157.2 > 95.2 1.278 0.038 0.040 > 3.01 2.63 1514.9 97.1 > 64.8 0.956 0.056 0.140 > 2.63 2.39 938.8 75.4 > 57.5 0.976 0.074 0.080 > 2.39 2.22 717.1 74.5 > 59.5 0.925 0.093 0.100 > 2.22 2.09 534.2 71.6 > 62.2 0.947 0.122 0.116 > 2.09 1.99 398.6 70.6 > 65.1 0.915 0.164 0.169 > 1.99 1.90 258.1 > 69.1 66.3 0.957 > 0.256 0.299 > > All reflections 1875.3 > 108.1 75.5 1.018 > 0.051 0.046 > > > > > > > > > > > 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 20, 2009, at 2:29 PM, James Holton wrote: > > > 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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