I didn't think I had anything to say on this, but following an
interesting discussion on a non-science based forum, I'd like to expand
on a point that both Dale and Felix made in different ways.
In the retraction of these 12 structures (and the 6 structures last
year), we are not seeing the
How very correct. And if anyone is doubt, remember the fiasco of the
'memory of water', published in Nature.
To borrow the title of DVD's talks, Just because its in Nature, it
does not mean its true.
More specifically, we are seeing peer review at work. I that the
implementation of peer
On Dec 16, 2009, at 7:40 AM, Anastassis Perrakis wrote:
How very correct. And if anyone is doubt, remember the fiasco of the 'memory
of water', published in Nature.
To borrow the title of DVD's talks, Just because its in Nature, it does not
mean its true.
Or, as one of my colleagues is
Dear Robbie, List,
This thread is steadily diverging. Apologies for my contribution to its
diversification.
snip
Who knows what they did to the maps in terms of (unwarrented) density
modefication to make them look cleaner?
The advantage of the EDS is that it is impartial and
uniform. The
I just scrapped most of my answer, Robbie was quicker, and I guess
Gerard is on holiday ;-)
As 'honorary Dutch' though here are my two cents.
It is only fair that a well-informed and well-educated human
being can do a better job than a fixed-frozen automated procedure.
This is exactly the
Not sure if in any of the 112 posts regarding either the retraction
theme or 'was 12 retraction' theme did mention, that after all despite
good or as good as possible refinement of the structure, the goal is
still to describe as accurately as possible the biological system
using
On Dec 13, 2009, at 11:00 AM, Jürgen Bosch wrote:
If you can't confirm your structure by solid biochemical or
biophysical methods what conclusions should you draw ?
Don't you wish it worked the other way in that every time someone had
a biochemical, physiological, or genetic result, they
:
Objet : Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Fred V wrote:
I personally like to visualise the electron density as well,
however, I do think that a non-crystallographer will go through the
trouble of downloading the structure factors, installing ccp4/coot
etc
Dear Fred,
People have already done this for all PDB entries:
- http://eds.bmc.uu.se/eds/ : maps and many crystallographic stats
- http://www.cmbi.ru.nl/pdb_redo : maps and re-refinement. And yes, the
stats and maps do improve most of the time, unfortunately also for
structures that are not
- Original Message -
From: Roger Rowlett rrowl...@colgate.edu mailto:
rrowl...@colgate.edu
Date: Thursday, December 10, 2009 21:07
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
This kind
Dear Fred,
People have already done this for all PDB entries:
- http://eds.bmc.uu.se/eds/ : maps and many crystallographic stats
- http://www.cmbi.ru.nl/pdb_redo : maps and re-refinement. And yes, the
stats and maps do improve most of the time, unfortunately also for
structures that are not
...@colgate.edu
Date: Thursday, December 10, 2009 21:07
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
This kind of unfortunate situation only reinforces the notion that
there must be some sort
...@pobox.com
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12
Structures=?UNKNOWN?Q?=FE?=
To: CCP4BB@JISCMAIL.AC.UK
Dear Fred,
People have already done this for all PDB entries:
- http://eds.bmc.uu.se/eds/ : maps and many crystallographic stats
- http://www.cmbi.ru.nl/pdb_redo : maps and re
Would the exact analysis of how each of these things were wrong and
fabricated be somewhere
available Would be fair (apart from the known case of C3b) to have
the whole analysis available
instead of just this kind of news feed. I suspect its not obvious by
five minute check in all cases.
11-Dec-2009 11:30 Rehovot
Dear All,
I Agree fully with Tommi, and feel, in parallel, we in the MX community must
think of better tools for referees to review papers and insist that these be
followed. For example we should insist on getting BOTH the coords and structure
factors for papers
Fraud is an arms race between the technology to perpetrate it and the
technology to detect it. In the end it is up to individual scientists
to act nobly and institutions to act vigilantly.
Speaking of the latter, where is the fallout from the Hellinga
debacle? Is everyone associated with
I uploaded an archive( pdf of emails plus text log files) of all the
conversations that took place around Eleanor Dodsons Original thread on
08/17/07 discussing the 2HR0 structure along with the attached log files
to an archive available at
Hi all,
Like everyone else, I was appalled.
My two cents worth: Nature and Science are not scientific journals in
the strict sense of the term. They are more like magazines (I won't go
all the way to say tabloids), and as such will do anything to publish
what seems to be hot. And will reject
The PDB is already taking action on this question by setting up
validation task forces for X-ray and NMR structures. I'm chairing the
X-ray task force, which is finally nearing completion of its report
after working on it since April 2008.
One of our recommendations (of most relevance to
Hey Tommi,
I am under the impression that Zbyszek Otwinowski has looked in depth
at all of the structures that have now been retracted and has prepared
a long manuscript detailing the evidence for fabrication and
falsification. As far as I know, this manuscript hasn't been
published yet
I think also the editors are sometimes to blame.
I once refereed a paper and pointed out that the resolution was overstated
(I/s(I) = 1.05 in the last resolution shell, as well as a couple of comments
that clearly suggested that the density wasn't very good). The editor
ignored my comments.
Hi Fred,
It could also be that the high impact factor of these journals, and their
'tabloid' character ensures that they are read by more people than other
journals. So any bad data or fraud that gets published in Nature, Cell or
Science is more likely to get noticed and talked about, than
It could also be that the high impact factor of these journals, and their
'tabloid' character ensures that they are read by more people than other
journals. So any bad data or fraud that gets published in Nature, Cell or
Science is more likely to get noticed and talked about, than something that
mailto:rrowl...@colgate.edu
Date: Thursday, December 10, 2009 21:07
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
This kind of unfortunate situation only reinforces the notion that
there must be some sort
, and Nature is one of the best-lit journals?
Phoebe
Original message
Date: Fri, 11 Dec 2009 13:36:38 +0100
From: Ganesh Natrajan natra...@embl.fr
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12
Structures
To: CCP4BB@JISCMAIL.AC.UK
Hi Fred,
It could also be that the high impact
, December 11, 2009 1:31 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
11-Dec-2009 11:30 Rehovot
Dear All,
I Agree fully with Tommi, and feel, in parallel, we in the MX community must
think of better tools for referees to review papers
You are absolutely right, more information describing to what extents these
structures were falsified will be valuable to the community. Actually, it
will be more useful if the investigators can publish their report as an
article in Acta D (as a case study for tracking falsified structures).
I
Ibrahim Moustafa wrote:
This will help to educate the non-crystallographers how to look at the
structures critically.
The first thing that a non-crystallographer should be aware of is the existence
of the temperature factors. It is a pity that the displays of biological
macromolecules on
Most of these structures can be easily identified as very suspicious in
a few seconds using POLYGON tool (Acta Cryst. D65, 297-300 (2009)); see
pictures here (courtesy of Sacha Urzhumtsev):
http://cci.lbl.gov/~afonine/fakes/Murthy-polygon-1.pdf
Pavel.
P.S. POLYGON tool is available as part
Not to derail the thread, but there is nothing, imho, wrong with I/s=1
cutoff (you expect I/s=2, I assume?). R-factors will get higher, but
there are good reasons to believe that model will actually be better.
This has been discussed many times before and there is probably no
resolution, so why
I think that when a model's resolution is clearly stated in a paper,
many readers still assume the pre-maximum likelihood definition (i.e.
high I/sigma, low Rsym in the high resolution shell). I've never seen a
paper where the I/sigma was given in the abstract after stating a
resolution.
I would like to point out that this outright fabrication remains an
isolated incident. There are over 50,000 crystal structures in the PDB,
which means that this is only ~0.02% of the total. This is all quite
bad, but let's not overstate the problem.
Maybe such report is not a great idea after
).
Engin
P.S. Oh well, the thread is hijacked now.
Original Message
Subject:Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Date: Fri, 11 Dec 2009 16:58:07 -0500
From: Christopher Bahl ccp4.b...@gmail.com
Reply-To: Christopher Bahl ccp4.b...@gmail.com
Fred V wrote:
I personally like to visualise the electron density as well,
however, I do think that a non-crystallographer will go through the
trouble of downloading the structure factors, installing ccp4/coot
etc.
Fred.
They shouldn't have to go through some of that trouble. Maps should
11, 2009 12:58 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Not to derail the thread, but there is nothing, imho, wrong with I/s=1
cutoff (you expect I/s=2, I assume?). R-factors will get higher, but
there are good reasons to believe that model
with not making too much of the resolution
limit, and presenting your statistics plainly and clearly in a table
(probably not buried in supplementary table 3).
Engin
P.S. Oh well, the thread is hijacked now.
Original Message
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
On Fri, 11 Dec 2009 15:30:53 -0500, Ibrahim Moustafa i.moust...@psu.edu wrote:
You are absolutely right, more information describing to what extents these
structures were falsified will be valuable to the community. Actually, it
will be more useful if the investigators can publish their report as
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Not to derail the thread, but there is nothing, imho, wrong with I/s=1
cutoff (you expect I/s=2, I assume?). R-factors will get higher, but
there are good reasons to believe that model will actually be better
Subject: RE: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Bernhard,
I understand that you are referring to the 2hr0, right? There the
Rmerge was unexpectedly low given the I/sigma. What I meant, of course,
is that I/sigma=1 is legitimate choice in general.
Ed.
On Fri, 2009-12-11 at 15:33
of Chemical Technology [IICT]
Tarnaka, Hyderabad
AP-500 607, INDIA
Tel:91-40-27191812
-- Original Message ---
From: Bernhard Rupp b...@ruppweb.org
To: CCP4BB@JISCMAIL.AC.UK
Sent: Fri, 11 Dec 2009 11:47:24 -0800
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
***
- Original Message -
From: Ibrahim Moustafa i.moust...@psu.edu
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, December 10, 2009 8:16 AM
Subject: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Hi all,
I want to share the following e-mail received from pdb-l.
It is sad to see something
He pretends to go to the synchrotron, comes back
Thats what I do all the time. Instead, I go to lane splitters /
jupiter for pizza and beer.
P
On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller j-kell...@md.northwestern.edu
wrote:
I assume this is the denouement of the Ajees et al debacle a while back?
Does this mean all authors on all of those papers were complicit? Otherwise,
how would one author alone perpetrate this kind of thing? He
This kind of unfortunate situation only reinforces
the notion that there must be some sort of laboratory
oversight/communication/mentoring/documentation procedures in place. In
my research lab (populated by a postdoc and a bunch of undergraduates)
raw images and data processing log files are
Rowlett rrowl...@colgate.edu
Date: Thursday, December 10, 2009 21:07
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
To: CCP4BB@JISCMAIL.AC.UK
This kind of unfortunate situation only reinforces the notion that there must
be some sort of laboratory oversight/communication/mentoring
Thanks for bringing this article to our attention. I went ahead and created
a table of the PDBs in question including links to the structures, journals
and citations. My hope is that it will save others time trying to track
down this information.
http://bit.ly/5KqaRF
Hope it helps.
Sean
. See this link:
http://www.biotechniques.com/news/Glycosylation-methods-paper-retracted/biotechniques-182060.html
Boaz
- Original Message -
From: Roger Rowlett rrowl...@colgate.edu
Date: Thursday, December 10, 2009 21:07
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12
:06 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Actually, I don't think that should be any consolation at all... As scientists,
from whatever field, we should be appalled by this kind of mischief from anyone
that calls themselves scientists
For previous debate on this issue see (in CCP4 archives)
https://www.jiscmail.ac.uk/cgi-bin/webadmin?S2=CCP4BBq=s=The+importanc
e+of+USING+our+validation+toolsf=a=b=
I think Eleanor started it
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0708L=CCP4BBP=R75676
And of course it is deja vu
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