But, the mistakes in the retracted work could have been avoided easily if
the person did the structure spent some efforts to understand/know what
he/she is doing! or if the authors asked for some help from professionals.

  Ibrahim
-- 

Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park,
Pennsylvania State University
PA 16802

Tel. (814) 863-8703
Fax (814) 865-7927



On 8/11/11 4:33 PM, "Maia Cherney" <[log in to unmask]> wrote:

> As the macromolecular crystallography becomes more automated and
> user-friendly many biologists learn to solve structures and they can
> make mistakes. Besides, new data become available that can give new
> ideas etc. I don't think that's so horrible to make an honest mistake
> and retract papers. Even great scientists sometimes published papers
> with wrong analysis.
> 
> Maia
> 
> On 11/08/2011 1:05 PM, Judith Murray-Rust wrote:
>> Just another point -  the macromolecular community are not the only ones with
>> a problem - I've just been shown
>> http://retractionwatch.wordpress.com/
>> which sheds some light on retractions. And also maybe says something about
>> why original data should be available/part of the  review process.
>> J
>> ________________________________________
>> From: CCP4 bulletin board [[log in to unmask]] On Behalf Of Gloria
>> Borgstahl [[log in to unmask]]
>> Sent: 11 August 2011 19:32
>> To: [log in to unmask]
>> Subject: Re: [ccp4bb] Another paper&  structure retracted
>> 
>> Dale, This is exactly the conversation  I just had with my student Jason,
>> right on!
>> The paper we are writing just now, this is figure 1.
>> But I always get rejected by Nature, so go figure.
>> On Thu, Aug 11, 2011 at 1:25 PM, Dale
>> Tronrud<[log in to unmask]<mailto:[log in to unmask]>>  wrote:
>>    I agree with Prof. Tomchick: if the point of your paper is your crystal
>> structure of
>> the binding of a ligand to a protein you should include a figure with the
>> omit map
>> (displayed without a "cover radius") that convinced you that binding took
>> place.  I
>> prefer that map over some simulated, after-the-fact, omit map calculated just
>> for
>> publication.
>> 
>>    This is not simply a matter for reviewers to be gatekeepers, it is
>> important for the
>> readers to know what level of confidence to place in this result, and it is
>> instructional
>> for everyone to see what ligand binding density looks like.  Apparently some
>> people don't
>> know what features to look for to distinguish between signal and noise.
>> 
>> Dale Tronrud
>> 
>> On 08/11/11 09:40, Diana Tomchick wrote:
>>> A quick glance at the header of the PDB file shows that there is one glaring
>>> discrepancy between it and the table in the paper that hasn't been mentioned
>>> yet in this forum. The data completeness (for data collection) reported in
>>> the paper is 95.7%, but in the header of the PDB file (actually, in both the
>>> 2QNS and the 3KJ5 depositions) the data completeness (for data collection)
>>> is reported as only 59.4%. The PDB header also contains an inconsistency,
>>> with the data completeness (for refinement) reported as 95.7%. Since the
>>> numbers of reflections reported for refinement versus data collection in the
>>> PDB header differ by less than 1%, it appears that there's been a bit of
>>> magical thinking that took place somewhere along the process from data
>>> processing to final model refinement. Small wonder that the refined geometry
>>> is so poor. Perhaps if these scientists had actually collected a complete
>>> dataset, we would not be having this conversation.
>>> 
>>> Diana
>>> 
>>> P.S. I have, on occasion, provided the coordinates and a map file to
>>> reviewers when they requested it. The last time it was requested was many
>>> years ago; I decided it was safer and easier if I provided as much
>>> information as possible in the manuscript (including better quality electron
>>> density figures than appear in this paper) to allow the reader to determine
>>> whether the work is valid or not.
>>> 
>>> * * * * * * * * * * * * * * * * * * * * * * * * * * * *
>>> Diana R. Tomchick
>>> Associate Professor
>>> University of Texas Southwestern Medical Center
>>> Department of Biochemistry
>>> 5323 Harry Hines Blvd.
>>> Rm. ND10.214B
>>> Dallas, TX 75390-8816, U.S.A.
>>> Email: [log in to unmask]
>>> 214-645-6383<tel:214-645-6383>  (phone)
>>> 214-645-6353<tel:214-645-6353>  (fax)
>>> 
>>> 
>>> 
>>> On Aug 10, 2011, at 5:45 PM, Dale Tronrud wrote:
>>> 
>>>>    I've made a quick look at the model and the paper - and it doesn't
>>>> need more than a quick look.  The description of the model in
>>>> the paper sounds great.  The problems in the model are clear.  My
>>>> favorite is the quote "Trp-477 of PTH1R makes several van der Waals
>>>> contacts with Trp-339 and Lys-337 of G-beta-1 ...".  They are "contacts"
>>>> all right.  The distances between the 477:CH2 and 337:CE is 2.75 A
>>>> and between 477:NE1 and 339:CH2 is 2.26 A.  There are many more.
>>>> 
>>>>    In general the geometry of this entire model is terrible.  In
>>>> Table 1 the bond length rmsd is listed at 1.64 A and the bond angles
>>>> are 0.0078 deg!  Perhaps one is to presume the numbers should be
>>>> swapped.  In any case, the values I calculate for the model are
>>>> 0.160 A and 4.46 deg!  Absolutely dreadful.  The PDB header lists
>>>> the (swapped) values from the paper and then reports hundreds of
>>>> outliers.
>>>> 
>>>>    The tools proposed by the Validation Task Force should cause a
>>>> model like this to pop out clearly.  Even the old tools show this
>>>> model is quite unreliable.  We just have to use them.
>>>> 
>>>> Dale Tronrud
>>>> 
>>>> On 08/10/11 14:35, Jacob Keller wrote:
>>>>> On the surface it doesn't seem as bad as others, i.e., it does not
>>>>> seem to be a real fake--perhaps just a strong form of wishful thinking
>>>>> and creative density interpretation. I wonder what would be a good
>>>>> metric in which to establish a cutoff for present/not present in
>>>>> density. CC, maybe?
>>>>> 
>>>>> Jacob
>>>>> 
>>>>> On Wed, Aug 10, 2011 at 4:01 PM, David
>>>>> Schuller<[log in to unmask]<mailto:[log in to unmask]>>  wrote:
>>>>>> Time to fuel up the gossip engines for the approaching weekend:
>>>>>> 
>>>>>> 
>>>>>> http://www.sciencedirect.com/science/article/pii/S096921260800186X
>>>>>> 
>>>>>> RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound
>>>>>> to
>>>>>> the G-Protein Dimer Gβ1γ2
>>>>>> Structure, Volume 16, Issue 7, 9 July 2008, Pages 1086-1094
>>>>>> Structure 2QNS withdrawn.
>>>>>> 
>>>>>> --
>>>>>> =======================================================================
>>>>>> All Things Serve the Beam
>>>>>> =======================================================================
>>>>>>                                David J. Schuller
>>>>>>                                modern man in a post-modern world
>>>>>>                                MacCHESS, Cornell University
>>>>>>             
>>>>>> [log in to unmask]<mailto:[log in to unmask]>
>>>>>> 
>>>>> 
>>>>> 
>>> 
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>>> 
>>> UT Southwestern Medical Center
>>> The future of medicine, today.
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