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. 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