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 > >
