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" <ch...@ualberta.ca> 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 [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Gloria >> Borgstahl [gborgst...@gmail.com] >> Sent: 11 August 2011 19:32 >> To: CCP4BB@JISCMAIL.AC.UK >> 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<det...@uoxray.uoregon.edu<mailto:det...@uoxray.uoregon.edu>> 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: diana.tomch...@utsouthwestern.edu >>> 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<dj...@cornell.edu<mailto:dj...@cornell.edu>> 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 >>>>>> >>>>>> schul...@cornell.edu<mailto:schul...@cornell.edu> >>>>>> >>>>> >>>>> >>> >>> ________________________________ >>> >>> UT Southwestern Medical Center >>> The future of medicine, today. >> >> NOTICE AND DISCLAIMER >> This e-mail (including any attachments) is intended for the above-named >> person(s). If you are not the intended recipient, notify the sender >> immediately, delete this email from your system and do not disclose or use >> for any purpose. >> >> We may monitor all incoming and outgoing emails in line with current >> legislation. 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