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Bernhard,
I would be worried about sending the structure factors and the coordinates
along with
the manuscript. Howev
Dear Felix
I agree - to address this Ash Buckle and colleagues have set up TARDIS
(http://tardis.edu.au/experiment/view/) and built the associated tools for
relatively painless deposition of data for registered users. As well as making
the data available to others we find that this is also a gr
In mathematics, when one is making a claim of solving the longstanding
mathematical problem, it is a tradition that his colleagues mathematician will
take care to check his solution. This solution MUST stood up to the scrutiny of
the world's expert. As an example see
http://en.wikipedia.org/wi
> What I meant, of course, is that I/sigma=1 is legitimate choice in general.
For refinement, yes, as long as the program weights them properly, and
your Rmerge is about 0.8/ in that shell.
High resolution cutoff in refinement should not be necessary
as long as the program applies proper bulk solv
Hi Ed
Negative and 0 Fobs are not allowed and they are removed from
consideration and flagged as unmeasured in the current version.
However you can have negative I (if you are using intensities in TWIN
mode). If you are using this after sampling the perhaps sampling
should be done using i
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 -0800, Bernhard Rupp wrote:
> There is nothing wrong per se wit
On Fri, 11 Dec 2009 15:30:53 -0500, Ibrahim Moustafa 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 an
>article in
I'm not arguing to exclude high resolution reflections. I just think
that authors shouldn't claim to have a 1.3 angstrom structure if they
have 0.5 I/sigma and 90% Rsym in the high resolution shell.
-Chris
--
Christopher Bahl
Department of Biochemistry
Dartmouth Medical School
7200 Vail Buil
There is nothing wrong per se with the cutoff level selected, but it is
the inconsistency of that level with Rmerge and the Rvalues for the
highest shell.
BR
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ed
Pozharski
Sent: Friday, December 1
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
Does anyone know if REFMAC has any SIGFP cutoff? I looked into manual
but perhaps missed it. What I mean is abnormal situation where some
FOBS are 0 or even negative - is there any intrinsic cutoff or
refinement will be done against all the reflections?
Thanks,
Ed.
--
Edwin Pozharski, PhD, Ass
I have to agree with Ed Pozharski here. It has been shown that it can be
valid to use I/sigma levels as low as ~1 for refinement (Ling, Read, et
al, Biochemistry 1998; Delabarre, Brunger, Acta Cryst D, 2006). I am
bothered more when I see I/sigma cutoffs of >4, where Rsym is <30% in
the high re
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 a
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. This
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 no
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 of
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 t
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 h
I have to say to the credit of Nature and competent authors that in
every case I have requested structure factors and coordinates for review
they have arranged to provide these. AFAIK this is their editorial policy,
but
it requires that at least one of the reviewers knows what to do
with the S
Yes, as much as I like to pick on the tabloids and their
somewhat iffy quality control, it looks like this guy got away
with faking structures for 10 years UNTIL he published in
Nature. Even Acta Cryst has egg on its face.
So the bottom line is that sunlight is indeed the best
disinfectant, and N
Paula Salgado wrote:
>
> 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. Not only it has
> effects on further research, delaying science sometimes b
Kevin,
1hps and 1hos do no appear to include Murthy as an author.
Since I need good as well as (very) bad examples for my molecular
modeling teaching,
I spent some time analyzing the structures which pdb codes you provided
with MolProbity.
All score very bad: high B factors, lots of clashes, ma
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
a
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 somethi
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.
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 (shame!),
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 t
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 rejec
Dear All,
on behalf of our Human Resources Department, I would like to forward a
posting for an open job in our Structural Biology team at Bayer Schering
Pharma AG.
For all details see the job posting below. Please do not reply to me but
to the contact given below, and also submit your applica
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
http://harijaycrystdata.s3.amazonaws.com/ccp4bb_archive
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 it
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 su
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.
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