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>
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