Dear Felix I agree - to address this Ash Buckle and colleagues have set up TARDIS (http://tardis.edu.au/experiment/view/) and built the associated tools for relatively painless deposition of data for registered users. As well as making the data available to others we find that this is also a great way of cleanly and permanently archiving the raw data! Furthermore, it seems that University libraries are keen to support electronic data deposition and archiving (not just Xtal data) in general, since their role in storing and providing access to paper journals is somewhat diminished!
J Felix Frolow <mbfro...@post.tau.ac.il> wrote: > In mathematics, when one is making a claim of solving the longstanding > mathematical problem, it is a tradition that his colleagues mathematician > will take care to check his solution. This solution MUST stood up to the > scrutiny of the world's expert. As an example see > http://en.wikipedia.org/wiki/Andrew_Wiles. Two papers of Wiles and > Wiles&Taylor's were published in Annals of Mathematics( both Nature and > Science do not publish mathematical papers probably due to the fact that > mathematicians were outcasted by Alfred Noble due to the unknown reason) > and were checked by international community. > It is pity, that when in MX society the similar claim/claims is/are made, > we do not have an access to all information needed to put this claim to > scrutiny as the policy of experimental data deposition is not very clear. > It would be convenient to have/to give an access to the data (not > necessarily raw) such as native and derivatives hkl, I, sigI files, all > with separated Friedel pairs and log files in PDF format of the scaling > programs, preferably in graphical form such as Report of HKL2000. This is > needed for the community to check and for desired for educational > purposes if one would like to reproduce the way of structure > determination of a difficult problem. > I personally have now idea what will be discovered in some most famous > cases, and probably as a result young structural biologists will be > reinforced in their believe that the structures could be derived from the > most marginal phase information such as in the case of > http://www.nature.com/nature/journal/v426/n6967/full/nature02200.html > > 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 Dec 12, 2009, at 24:27 , Ed Pozharski wrote: > >> I would like to point out that this outright fabrication remains an >> isolated incident. There are over 50,000 crystal structures in the >> PDB, >> which means that this is only ~0.02% of the total. This is all quite >> bad, but let's not overstate the problem. >> >> Maybe such report is not a great idea after all - don't you think it >> will help the next troublemaker to fabricate structures better? :) >> >> I wonder if there are any structures from the author in question that >> were not fabricated. After all, some serious mistakes were made in >> 2hr0 >> (how can you not know about bulk solvent and B-factor variation?). >> There is 1BGX which was not on retraction list (I guess since it was >> "done" at Temple University, not UAB), but it looks weird too: the >> B-factors of main chain and side chain atoms are not much different >> from >> each other and this 2.3A-diffracting crystal has very few crystal >> contacts (it's the Taq DNA polymerase in complex with inhibitory Fab >> and >> the whole heavy chain makes no crystal contacts at all which is >> probably >> unique). >> >> On Fri, 2009-12-11 at 15:30 -0500, Ibrahim Moustafa wrote: >>> You are absolutely right, more information describing to what >>> extents these >>> structures were falsified will be valuable to the community. >>> Actually, it >>> will be more useful if the investigators can publish their report >>> as an >>> article in Acta D (as a case study for tracking falsified >>> structures). >>> >>> I have a suggestion (actually a request) to the expertise in the >>> field to >>> write a kind of review article about "sources of error in >>> crystallography >>> and how to hunt these errors". It will be even better if it is >>> written >>> considering the non-crystallographers (scientists who use the >>> structural >>> information - like the co-authors on structural papers). This will >>> help to >>> educate the non-crystallographers how to look at the structures >>> critically. >>> >>> Ibrahim >>> >> >> >> -- >> Edwin Pozharski, PhD, Assistant Professor >> University of Maryland, Baltimore >> ---------------------------------------------- >> When the Way is forgotten duty and justice appear; >> Then knowledge and wisdom are born along with hypocrisy. >> When harmonious relationships dissolve then respect and devotion >> arise; >> When a nation falls to chaos then loyalty and patriotism are born. >> ------------------------------ / Lao Tse / -- Professor James Whisstock ARC Federation Fellow Honorary NHMRC Principal Research Fellow Department of Biochemistry and Molecular Biology Monash University, Clayton Campus, Building 77, VIC, 3800, Australia +613 9902 9312 (Phone) +613 9902 9500 (Fax) +61 418 170 585 (Mobile)
