After consultation with Ton Spek, I should correct my last email. It turns out that my 'watermark' was not clever enough, because PLATON - his program used to make the picture that I had randomly picked as an example - can emulate the XP watermark (the way of shading the ellipsoids which I intended to be different from the 'genuine ORTEP') rather well, and had indeed done so in the picture in question. However it is technically an 'ORTEP clone' (like XP), not an 'XP clone'. I am using 'clone' to mean that one has intentionally created the 'same look and feel' as an existing program, not to imply that the same code is used.
This shows how difficult it will be for James to include an unforgeable 'watermark' in his calculated frames, though I would still encourage him to try. Being able to emulate the experiment so well is wonderful for debugging the programs used to process the frames, but it will surely make fraud more difficult to detect! George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Fri, 20 Mar 2009, George M. Sheldrick wrote: > Dear James, > > About 30 years ago I wrote a clone of the program ORTEP; the clone > was called XP, but unfortunately Microsoft later stole the name > and brought it into disrepute. So that I would always be able to > see at a glance which plots were 'genuine ORTEP' and which were > my clone, I built in a sort of watermark (a slightly different way > of shading the ellipsoids). I hope that you have done something > similar in mlfsom! But please don't reveal what it is to ccp4bb, > I suggest that you deposit the information in encripted form with > the PDB. Otherwise you may suffer the same fate as I did: the > 'ORTEP' plot on the cover of the February 2009 Acta C appears to > have been made by a clone of my clone! > > The information that data produced by mlfsom give Rcryst ~ Rsym > is very interesting and makes it even more likely that the > typical R-values of 19.9% for proteins have something to do with > the ca. 50% of the structure that is rather poorly modeled - the > 'solvent' region. > > Best wishes, George > > Prof. George M. Sheldrick FRS > Dept. Structural Chemistry, > University of Goettingen, > Tammannstr. 4, > D37077 Goettingen, Germany > Tel. +49-551-39-3021 or -3068 > Fax. +49-551-39-22582 > > > On Fri, 20 Mar 2009, 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 > > > > >
