While the topic of "fabrication" is still hot, I thought I too could add
a few thoughts.
Our Mathematician friends always make fun of us (Biologists/ Biochemists/
crystallographers!) that our papers are accepted within 4-8 weeks of
submission.
This is not to talk of Science/ Nature/ Cell, whe
Storing all the images *is* expensive but it can be done - the JCSG do
this and make available a good chunk of their raw diffraction data. The
cost is, however, in preparing this to make the data useful for the
person who downloads it.
If we are going to store and publish the raw experimental meas
On Thu, Aug 16, 2007 at 11:31:00PM -0400, Petr Leiman wrote:
> A small, but very important excerpt from the original Randy Read's message
>
> "... Nature did not allow us to use the word "fabricated". Nor were we
> allowed to discuss other structures from the same group, if they weren't
> publis
Dear colleagues,
the recent discussion on the necessity and feasibility of storing raw
data for all our structures raises a second point, I think. For the
current discussion it is only a matter of storage place that has to be
assigned somehow to make fobs, unmerged data, or raw images availab
Hi
for data generation rates I can give you an idea of what is generated at a
Bending magnet beamline at ESRF
For 2006 at BM14 we and our users generated 266997 images/frames from our
MAR225 CCD (18mb files) or in other words ~4.8Tbyte (if you have patience to
do so then bzip2 will reduce these r
Hi Matrin,
On Fri, Aug 17, 2007 at 11:09:28AM +0200, Martin Walsh wrote:
> For 2006 at BM14 we and our users generated 266997 images/frames from our
> MAR225 CCD (18mb files) or in other words ~4.8Tbyte (if you have patience to
> do so then bzip2 will reduce these raw images to between 5.5 and 7Mb
how about this scenario:
the structure really is as published, or very like it, but upon
refinement, R-factors were high, other indicators were dodgy etc. so
the authors were afraid to publish as is and made up a dataset to
support their structure - this would be a bit less bad.
let's see
I'm with Bill on this one.
Despite the overwhelming evidence, one must still keep in mind that the
accused, including all authors on the manscript for this structure, have yet to
be 'convicted' in any legal sense. I hope the investigation is swift, thorough
and leads to clear conclusions and
Hi Clemens, yes I was not suggesting we keep the 'junk' but gave the brute
figures more to give an idea for people to see how much data is collected.
But you are right I should of qualified -for those 266,997 images I
estimated 1163 data collections (where i classified a data collection as a
set o
Dear fellow crystallographers,
I'd like to add yet another piece to the ongoing discussion about C3b
& Co., and the importance of submitting diffraction images in
addition to structure factors.
Partly in response to some letters that had just appeared in the same
journal, on 16 July toget
Dear all,
It has been quite fascinating to see this thread develop in the past
couple of days, as I was a hair's breadth away from initiating a similar
thread upon returning from the ACA meeting at the end of July.
An impromptu working dinner was held on the Tuesday evening of the
meeti
On Aug 17, 2007, at 8:36, George M. Sheldrick wrote:
Dominika is entirely correct, the F and (especially) sigma(F) values
are clearly inconsistent with my naive suggestion that columns could
have been swapped accidentally in an mtz file.
Since the sigma(f) issue has been raised, let me elabora
Just to be clear on my previous email, I encourage all evidence to be
gathered, posted and accumulated for proper evaluation of this case. It
will prove incredibly useful for all involved as this case moves
forward.
It is also proving useful for course development - frankly, I am
accumulating
Dear group members,
I'd like to bring following opening to your attention:
'Application Specialist - X-Ray Crystallography for Life-Science
Bruker is seeking for its Singapore Expertise Centre an individual to
support our regional sale force in the sales and marketing of our x-ray
crystallog
Before going into an ethics class, I think this material needs to go into a
crystallography class. Every crystallographer (and maybe even every
structural biologist) should know why the structure is fishy, how fishiness
can be detected, how one can make sure one's own structure is legit, etc.
Anal
After Richard Reid more than 100 million people each year
have to have their shoes examined and one effect is that older
buildings like Heathrow Terminal 3 is the most painful place on earth,
the cost of someone trying light their shoelaces has affect us all.
The discussion on archiving image dat
Since there are several sub-plots in that mammoth thread, I thought
branching out would be a good idea.
I think working out the technicalities of how to publicly archive raw
data is fairly simple compared to the bigger picture.
1. Indeed, all the required meta-data will need to be captured
I will be out of the office starting 08/01/2007 and will not return until
08/31/2007.
I will respond to your message when I return.
I have read the comments in Nature and on the CCP4BB with excitement,
almost the same level of excitement with which I followed this year's
Tour de France. Speaking of which, I can see many analogies.
Political correctness aside, what is the meaning of an (internationally
acclaimed) journal if
Hi Kim,
On Fri, Aug 17, 2007 at 03:04:27PM +0100, Kim Henrick wrote:
> The discussion on archiving image data sets -
> I guess that less than 1% of the image sets for PDB entries
>are useful to software development (and can be got privately)
I would think much much more would be useful for s
Hi,
On the question of a "uniform format" for this data, I believe that
imgCIF has been working towards this end for a number of years. As a
very vocal supporter of this I would like to say that this is an ideal
archival format for the following reasons:
- the terms are clearly defined (or are c
I am trying to keep track of, and notes on these Emails, many of which
raise very important Qs for our community, much more so than any
problems with a particulat structure..
But it would be a lot easier if you would all stick to the same Subject
header!!!
Eleanor
Phoebe,
Any and every reviewer has right to request the coordinate file as well
as sf file.
The other question is: Why most of them are not exercising their rights?
Vaheh Oganesyan
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Behalf Of
[EMAIL PROTECTED]
Sent:
I don't think all journals have that policy, and even so, making the
reviewers specifically request the data implies to the reviewees that
somebody out there doesn't trust them.
You shouldn't have to insult the authors in order to do a proper
reviewing job - you should just be able to download
Hi Elisabetta
Your unit cell is pseudo F222, with twin law (-h,-k,h+k+l):
iotbx.explore_metric_symmetry --unit_cell="47.7533.6191.04
90.000 103.635 90.000" --space_group=C2
(output below)
Did you rule out twinning?
Try runing phenix.xtriage for some intensity stats and/or
phenix.refine
There are obvious ones like - incomplete structure etc, but have you
tried TLS? Sometimes this can dramaticaly improve the R factors.
You seem to have lost of lot of the low resolution data - could this
mean you had overloads which naybe could be rescued.. That can down
grade the maps a good
On the question of what is "trivial" I would argue that deposition of
the raw diffraction images is not - for a few simple reasons:
- if I deposit structure factors with my model it is very
straightforward to run an analysis tool which will confirm that model
and I/F belong together. Without a pr
Dear all,
I have a structure at 1.6A. At the end of refinement the Rfactor and Rfree
are quite high (23/29.6%). Here are some info:
Morphology of crystals: large but thin plates (150 x 400 x 20 microns)
Number of residues: 160 (2 x 80); 103 water molecules
Space group: C2
Unit Cell: 47.7533.6
I suggest that it is not neccessary to submit all images for a reasonable review
of a crystallography paper.
Submission and storage of a "few" images at the start of a data collection and a
"few" from the end, along with (1) unmerged F or I, including all reflections
that are systematic absences f
> how about this scenario:
> the structure really is as published, or very like it, but upon
> refinement, R-factors were high, other indicators were dodgy etc. so
> the authors were afraid to publish as is and made up a dataset to
> support their structure - this would be a bit less bad.
>
pardon
Providing a centralized archive of raw data for crystallographic
images would be a great asset to everyone, but most especially to the
original investigator.
I'm reminded of a conversation held with one of my postdoctoral
mentors back in the mid 1990's. She was gazing at the rows of reel-to
I think having each lab deal with archiving their own data and making
them available to the public is much less practical than having a
centralized repository for the following reasons:
1. The overhead would be many times that of a centralized repository,
because of multiplication of effort
Hi all,
I'm certain this can be done, but I figure it would be much easier asking
the news group than spending hours trawling though random web pages:
Does anyone know how to search protein sequence databases using a consensus
sequence which allows varying gap sizes, and homologous amino acid
The proper choice of reviewers is important, but perhaps some of the
burden for fact checking should be shifted to the journal. Some
journals are already doing image analysis to check gels/microscopy
images, and there is no reason why this cannot be extended for structures.
In practical terms
On Fri, August 17, 2007 10:56 am, Eleanor Dodson wrote:
> There are obvious ones like - incomplete structure etc, but have you
> tried TLS? Sometimes this can dramaticaly improve the R factors.
>
When people run TLS, are they trying to improve the R-factors, or actually
generate a reasonable mo
The proper choice of reviewers is important, but perhaps some of the
burden for fact checking should be shifted to the journal. Some
journals are already doing image analysis to check gels/microscopy
images, and there is no reason why this cannot be extended for structures.
In practical terms
Hi Paul,
Look at the syntax for prosite patterns. It will
do what you want. There are probably
better syntax rule descriptions / tutorial, but
here is a quick link...
http://ca.expasy.org/tools/scnpsit3.html#patsyntax
E.g. you can search with a pattern like
'D-x(2,4)-D-[N,Q]'
Regards,
Mitch
Santarsiero, Bernard D. wrote:
On Fri, August 17, 2007 10:56 am, Eleanor Dodson wrote:
There are obvious ones like - incomplete structure etc, but have you
tried TLS? Sometimes this can dramaticaly improve the R factors.
When people run TLS, are they trying to improve the R-factor
How about the Petabox:
http://www.capricorn-tech.com/
"Capricorn Technologies was founded in 2004 and provides petabyte-class storage
solutions for organizations worldwide. Capricorn's PetaBox technology grew out
of a search for high density, low cost, low power storage systems for the
world's
While all of the comments on this situation have been entertaining, I've been
most impressed by comments from Bill Scott, Gerard Bricogne and Kim Hendricks.
I think due process is called for in considering problem structures that may or
may not be fabricated. Public discussion of technical or cr
Hi Ed:
On Aug 17, 2007, at 10:43 AM, Edwin Pozharski wrote:
Bill,
presumption of innocence applies when person's life or freedom is
at stake, other words - when you are accused of a crime. It does
not apply in many other circumstances (for instance, when applying
for short-term visa to
I'm trying to keep up with all the email on this discussion so someone
may have posted this already. If so I apologise (or apologize as
appropriate).
With quite appropriate timing Brown and Ramaswamy have just published a
very nice paper in Acta D. on the quality of Protein Structures -
http://jou
CCP4 bulletin board wrote on 08/17/2007 07:38:00
AM:
>
> Thus, I analyzed the distribution of the experimental sigmas in three
> structures:
> 1E3M and two structures of mine at the same resolution (1CTN, 1E3M)
>
> The results are in:
>
> http://xtal.nki.nl/nature-debate/
>
>
To add my two cents
This will have to be automated, and not subjectively flagged by the
editors - something just like EDS ("review-EDS"?), where the data
submitted gets sent automatically by the journal to an EDS type server,
and the results are available only to the reviewers.
The reviewers should be able to log
It seems that a public discussion with points and counterpoints
presented openly and fairly is in complete adherence to the ideals of
due process. Since this discussion is not deciding the criminal fate of
any individual, it does not seem necessary to defer it to any political
government. Also,
Before we all come up with a solution of archiving all the images to
bury them in a safe place, we should find an immediate cure.
Attention to Nature and Science:
I have a solution for the continued publication of wrong structures
in big journals. Every structural manuscript submitted to a h
The PDB is missing a business opportunity. If authors pay
1000s of dollars for publication in high impact journals,
they might as well pay a few bucks for image deposition.
If I could get my images stored reliably and perpetually
for something like $20-50 a pop, I'd do it. Do you know
where your f
IANAL, but I have been advised by lawyers in highly similar situations.
Publicly accusing someone of either criminal fraud and/or academic
fraud is serious business, and it is certainly something that could
get you prosecuted for criminal libel, as the accusation will likely
have the effect
On 17 Aug 2007, at 20:51, William Scott wrote:
To follow the legal analogy, does the letter of Gros et al. proves
beyond reasonable doubt that the structure in question is indeed a
fabrication? As you said, it is a compelling case.
No, I said it "appears" (to me) to be "a compelling case",
All theories or models are wrong until proven otherwise. We all need
to stand up to support the ideas we try to put into press or admit that
we cannot satisfy their critics. (Not "our critics", this process should
not be personal). I agree with Nature's editors that questions of
"fabrication
FWIW, I don't agree with storing image data, I don't think they justify the
cost of storage even remotely (some people debate the value of the structures
themselves)...but if you want to do it anyway, maybe we should use a format
like jpeg2000.
Last time I checked, none of the major image p
I think I can speak from experience on the topic of archiving image
data. I have ~40,000 DVD-R disks in my office. This represents:
6 years of data collection at ALS 8.3.1
60 TB of data (>99% of everything collected, 2 copies)
10,000 data sets
318 PDB entries
$4000 of media
The purposes of t
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