Dear All,
It is worth remembering the exemplary manner in which David Eisenberg and his
group followed up on the flawed structure of
rubisco that they published. First, David gave a long talk at the Diffraction
Gordon Conference explaining in detail how the
error arose, and offering clear suggestions to the community on how to avoid
similar mistakes. Second, the rubisco structure
led the group to develop 3-d profiling, sure one of the most powerful tools we
have for evaluating a structure.
Thus was a error transformed into a powerful methdologcal tool to minimize the
frequency of errors in the future.
----- Original Message -----
From: Boaz Shaanan <[EMAIL PROTECTED]>
Date: Saturday, December 23, 2006 5:12 pm
Subject: Re: [ccp4bb]: Retraction of ABC transporter structures - were
there warning signs?
To: William Scott <[EMAIL PROTECTED]>
Cc: [email protected]
>
> My impression is that it's the case of "hot" structures NOT being
> checked carefully. A while ago, after wrong (unrefined or poorly
> refined) structures of Ras and Rubisco were published it became
> customary to not accept structures if the R (Rwork at the time, Rfree
> was introduced later) wasn't below 0.25 together with proper fit to
> Ramachandran plot. Later Rfree was introduced and another measure of
> caution helped to filter out wrong structures. In the last few years
> several "hot" structure were allowed to be published (in Science,
> Nature and Cell, of course) with horrensdous agreement R-factor, the
> publication being justified solely, I suppose, based on their
> "hotness". (as I recall the MacKinnon structure of the K-channel was
> the first in the series). There is of course a case for difficult,
> most interesting and "hot" structures, to be published in prestigious
> journals but they should be checked very carefully, sometimes with
> other (additional) measures than the standard ones. It's for the hot
> journals to work harder on refereeing those articles.
>
>
> Boaz
>
>
> ----- Original Message -----
> From: William Scott <[EMAIL PROTECTED]>
> Date: Saturday, December 23, 2006 22:19
> Subject: Re: [ccp4bb]: Retraction of ABC transporter structures - were
> there warning signs?
> To: [email protected]
>
> > *** For details on how to be removed from this list visit
> > the ***
> > *** CCP4
> > home page
> > 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
> > statisticsdon't scream out that there is a problem.
> >
> >
> >
> >
> >
> >
> >
>
> Boaz Shaanan, Ph.D.
> Associate Professor
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> Israel
> Phone: 972-8-647-2220 ; Fax: 646-1710
> Skype: boaz.shaanan‎
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