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David J. Schuller wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > On Sat, 2006-12-23 at 13:32 -0500, Arun Malhotra wrote: > >> I was shocked to see the retraction in yesterday's issue of Science (Dec >> 22, 2006) of several ABC transporter structures and papers from the >> Chang lab, including three published in Science. The retraction says >> that the structures have the wrong hand and topology due to an >> "in-house" program that inverted the signs on the anomalous pairs. >> >> I have no expertise in ABC transporters, but were there warning signs in >> the structures? Were red flags raised by PDB or the other servers such >> as EDI, EDS, etc.? Looking at some of these papers, these are low >> resolution structure and I see very high R/Rfree, but there must have >> been other signs of problems as well. >> >> In the past few years, there have been almost no structures retracted >> due to gross errors and the checks being used by structural biology >> community seemed to working quite well - what can we learn from this >> tragic and sad error ? >> > > One thing we can learn is that a high-profile journal reporting on this > fiasco (http://www.sciencemag.org/cgi/content/full/314/5807/1856 Science > 22 December 2006:Vol. 314. no. 5807, pp. 1856 - 1857 DOI: > 10.1126/science.314.5807.1856), after having accepted three such botched > structures for publication, can find no room to criticise itself and > other high-profile journals. I believe the race between Science, Nature > and other top journals to get the hottest, sexiest articles has > contributed to their overlooking the solidity of the underlying work. > It sounds like an honest mistake, and it is not clear to me that the journal is at fault (unless they picked incompetent reviewers). The real question is whether this happens more frequently, but perhaps only the "hot" structures get double-checked. It is also asking a lot of the reviewers (and therefore the journal) to pick up on a mistake that the authors themselves presumably gladly would have done themselves if it had been more obvious. Again, maybe the best thing is to provide pdb, Fobs, exptl phases and maps to the referees. I do this now. At least one referee thanked me for it. It's also probably a good idea to use more than one software suite to reproduce the phasing and refinement, and check the answer with a SA composite omit map and/or EDEN for consistency. (EDEN has a phase perturbation function that is helpful.) Consistency doesn't equal truth, but if two similar programs give widely disparate results, it is a tipoff that something might be seriously amiss, even if the numerical statistics don't scream out that there is a problem.
