Does anyone here know what, if anything, happened with the whole Ajees et
al. debacle? Just swept under the carpet, lost in the mists of time?
Jacob Keller
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laborato
Think this bounced last time I tried to mail it in, a simulator exists at:
http://fable.sourceforge.net/index.php/Farfield_Simulation
Jon
Eleanor Dodson wrote:
ZO has a good point - it is a pain trying to get decent simulated
material - maybe there is an employment opportunity here?
Eleanor
ZO has a good point - it is a pain trying to get decent simulated
material - maybe there is an employment opportunity here?
Eleanor
Zbyszek Otwinowski wrote:
James Holton wrote:
How MUCH do you want to bet?
;)
Any amount, as long as we are taking about real diffraction images
correspondin
Just to add to Raji and Dave¹s comments. It seems to me that over the last
5-10 years learning theory has indeed been discouraged, takes up to much
time etc. This can be seen in changes that have occurred to the advice
given when writing up a thesis. People used to write a theory chapter where
t
I'm going to agree with Raji's observations, and fan the flames of his point
a little.
I count myself as lucky that I have had access to certain people during my
crystallographic training who had a good understanding of the theory behind
crystallography (hopefully I have exploited this luck suffi
I would like to mention some other issues now that Ajees et al. has stirred all
sorts of
discussions. I hope I haven't opened Pandora's box.
>From what I have learned around here, very often, there seems to be little
>time allowed or allocated
to actually learn--a bit beyond the surface--some of
Could such solvent ordering be a byproduct of unusually low solvent
content as both of the structures seem to have (1h6w & 1ocy)? Perhaps
cryoprotectant did not penetrate the solvent channels, but the
crystal maintained its integrity nevertheless?
On Aug 28, 2007, at 1:14 AM, Kevin Cowtan
Wow! Those are two pretty amazing structures.
For those of you who haven't had a look, the ordered molecules are in
layers with *huge* gaps in between, much greater than in 2hr0.
And yet both of these structures were solved with experimental phasing
(SIRAS) unlike 2hr0, and the data is to hig
an wrote:
- Original Message - From: "Jenny Martin"
<[EMAIL PROTECTED]>
To:
Sent: Thursday, August 23, 2007 5:46 PM
Subject: Re: [ccp4bb] The importance of USING our validation tools
My question is, how could crystals with 80% or more solvent
diffract so well? The be
ugust 23, 2007 5:46 PM
Subject: Re: [ccp4bb] The importance of USING our validation tools
My question is, how could crystals with 80% or more solvent diffract
so well? The best of the three is 1.9A resolution with I/sigI 48
(top shell 2.5). My experience is that such crystals diffract very
we
- Original Message -
From: "Jenny Martin" <[EMAIL PROTECTED]>
To:
Sent: Thursday, August 23, 2007 5:46 PM
Subject: Re: [ccp4bb] The importance of USING our validation tools
My question is, how could crystals with 80% or more solvent diffract so
well? The best of t
In the cases you list, it is clearly recognized that the fault lies
with the investigator and not the method. In most of the cases where
serious problems have been identified in published models the authors
have stonewalled by saying that the method failed them.
"The methods of crystallogr
I've been reading the contributions on this topic with much interest.
It's been very timely in that I've been giving 3rd year u/g lectures
on protein X-ray structures and their validation over the past week.
As part of the preparation for the lectures, I searched the PDB for
structures with hi
How MUCH do you want to bet?
;)
-James Holton
MAD Scientist
Anastassis Perrakis wrote:
On 23 Aug 2007, at 18:17, Zbyszek Otwinowski wrote:
I 100% agree with Jordi Benach. However, the problem with idea is that
it requires the real images in question to exist. I am willing to
take any bet
James Holton wrote:
How MUCH do you want to bet?
;)
Any amount, as long as we are taking about real diffraction images
corresponding to the deposited file with "observed" structure factors.
I doubt that simulated diffraction images will be shown, because they
are easy to be recognized as such
On 23 Aug 2007, at 18:17, Zbyszek Otwinowski wrote:
I 100% agree with Jordi Benach. However, the problem with idea is that
it requires the real images in question to exist. I am willing to
take any bet
that they will never be shown to the public.*
Since by taking bets, one simply prefers on
I 100% agree with Jordi Benach. However, the problem with idea is that
it requires the real images in question to exist. I am willing to take any bet
that they will never be shown to the public.*
Jordi Benach wrote:
Dear colleagues,
1) I think Ajees et al. should make available the raw diffract
Dear colleagues,
1) I think Ajees et al. should make available the raw diffraction images of
the structure in paper that has caused so much literary commotion, unless
they haven't already done so. Perhaps simply put them in an open ftp server?
As I imagine, unless I have missed something, these
Mischa,
I don't think that the field of nanotechnology crumbled when allegations
against Jan Hendrik Schon (21 papers withdrawn, 15 in Science/Nature)
turned out to be true. I don't think that nobody trusts biologists
anymore because of Eric Poehlman (17 falsified grants, 10 papers with
fa
Phil,
A few points:
1. The recent erroneous structures that I'm aware of had either extremely
high free R values ( 40 - 45%) or unreasonably low free R values (low
twenties) despite the presence of > 80% solvent and gaps in crystal
packing.
2. At low resolution (3.5 A and lower) , maps can
package or the wwPDB annotators.
Regards,
Mitch
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Boaz Shaanan
Sent: Sunday, August 19, 2007 2:38 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools
Curious
I worry a bit about some of this discussion, in that I wouldn't like
the free-R-factor police to get too powerful. I imagine that many of
us have struggled with datasets which are sub-optimal for all sorts
of reasons (all crystals are multiple/split/twinned; substantial
disordered regions;
Dear Alex,
Of course a simplified one page summary would not be the last word, but I
think that it would be a big step in the right direction. For example a
value of Rfree that is 'too good' because the reflection set for it has
been chosen wrongly can be detected statistically (Tickle et al.,
I do not think the small molecule approach proposed by George Sheldrick
is sufficient for validation of protein structures, as misrepresentation
of experimental statistics/resolution is hard to detect with it, and
these factors appear to play crucial role in defining the fate of many
hot structures
k" <[EMAIL PROTECTED]>
Date: Saturday, August 18, 2007 15:27
Subject: Re: [ccp4bb] The importance of USING our validation tools
To: CCP4BB@JISCMAIL.AC.UK
> There are good reasons for preserving frames, but most of all
> for the
> crystals that appeared to diffract but d
PS. A completely unimportant correction to my comment on the MolProbity
output for 2HR0: every residue is indeed an outlier in at least one test,
but in three cases it is only the CB-deviation test, not the other three
tests that I mentioned.
George
Prof. George M. Sheldrick FRS
Dept. Structu
Dear all,
I agree with MM about the ligand and complex structures. Even in the
most honest circumstances, it is easy to get carried away with hopes and
excitement. My personal embarassing experience was some years ago. It
involved a protein that I had crystallized in a different space group in
the
-Original Message-
From: Kantardjieff, Katherine
[mailto:[EMAIL PROTECTED]
Sent: Friday, August 17, 2007 4:55 PM
To: [EMAIL PROTECTED]; Dale Tronrud
Subject: RE: [ccp4bb] The importance of USING our validation tools
Since my name appeared in this email exchange, I thought I should
OTECTED] On Behalf Of
Juergen Bosch
Sent: Saturday, August 18, 2007 12:20 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools
Hi Mischa,
I think you are right with ligand structures and it would be very
difficult if not impossible to distinguish between
-Tom
-Original Message-
From: CCP4 bulletin board on behalf of George M. Sheldrick
Sent: Sat 8/18/2007 6:26 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools
There are good reasons for preserving frames, but most of all for the
crystals that a
Hi Mischa,
I think you are right with ligand structures and it would be very
difficult if not impossible to distinguish between real measured data
and faked data. You just need to run a docking program dock the ligand
calculate new structure factors add some noise and combine that with
your r
I agree. However, I am personally not so much worried about entire protein
structures being wrong or fabricated. I am much more worried about
co-crystal structures. Capturing a binding partner, a reaction
intermediate or a substrate in an active site is often as spectacular an
achievement as de
y long thread even longer.
Artem
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of George
M. Sheldrick
Sent: Saturday, August 18, 2007 9:27 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools
There are good reas
There are good reasons for preserving frames, but most of all for the
crystals that appeared to diffract but did not lead to a successful
structure solution, publication, and PDB deposition. Maybe in the future
there will be improved data processing software (for example to integrate
non-merohe
it is still very bad, but at least it would mean there was some
experimental
evidence for the model and it was not completely made up.
Mark
Mark J. van Raaij
Unidad de Bioquímica Estructural
Dpto de Bioquímica, Facultad de Farmacia
and
Unidad de Rayos X, Edificio CACTUS
Universidad de Santiago
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
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",
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
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
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,
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
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
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
> 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
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
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
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
-
From: Clemens Vonrhein [mailto:[EMAIL PROTECTED]
Sent: Friday, August 17, 2007 12:00 PM
To: Martin A. Walsh
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools
Hi Matrin,
On Fri, Aug 17, 2007 at 11:09:28AM +0200, Martin Walsh wrote:
> For 2006 a
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
ehalf Of
Clemens Vonrhein
Sent: Thursday, August 16, 2007 4:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools
On Thu, Aug 16, 2007 at 03:13:29PM +0100, Phil Evans wrote:
> What do you count as raw data? Rawest are the images - everything
>
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
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Phil Evans
Sent: 16 August 2007 15:13
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools
What do you count as raw data? Rawest are the images - everything beyond
that is modellling - but archiv
M: Randy J. Read <[EMAIL PROTECTED]>
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools
On Aug 16 2007, Eleanor Dodson wrote:
>The weighting in REFMAC is a function of SigmA ( plotted in log file).
>For this example it will be nearly 1 for all
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.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D
On Thu, 16 Aug 2007, Clemens Vonrhein wrote:
Maybe we should contact Google to let them do it for us ;-)
Better yet, simply download your images to a computer that uses AT&T as an
internet service provider. All the information will be automatically
copied and stored by the NSA
No one knows definitively if this was fabricated.
Well, at least one person does.
But I agree, it is important to keep in mind that the proper venue for
determining guilt or innocence in the case of fraud is the court system.
Until fairly recently, the idea of presumed innocence and the
I like to emphasize that the infamous table 1 alone should
have immediately tipped off any competent reviewer.
The last shell I/Isig is 1.3 and rmerge 0.11 (!).
And keep in mind that this statistics comes from
merging data from FOUR different crystals! (That's
clearly and unambigously stated in
Due to these recent, highly publicized irregularities and ample
(snide) remarks I hear about them from non-crystallographers, I am
wondering if the trust in macromolecular crystallography is beginning
to erode. It is often very difficult even for experts to distinguish
fake or wishful think
A few thoughts following on Richard Baxter and George Sheldrick . . .
Re: gaps in the lattice see the tyr-tRNA synthase structures (1tya for
example). Fersht has written a whole book full of insights from these
structures.
Re: Phaser Z scores. For some MR work with two xtal forms of a str
There are several issues under current discussion. We
outline a few of these below, in order of importance.
The structure 2hr0 is unambiguously fake. Valid arguments
have already been published in a Brief Communication by
Janssen et. al (Nature, 448:E1-E2, 9 August 2007). However,
the publish
stallography. I actually gave a
>> homework assignment that was simply to sign up for the ccp4bb.
>>
>> In reference to the previously mentioned work, I'd also like to hear
>> discussion concurring or not the response letter some of which seems
>> plausible to me.
&g
The deposited structure 2HR0 shows all the signs of having been refined,
deliberately or accidentally, against 'calculated' data. The model used
to 'calculate' the data had (almost) constant B-values in a rather empty
cell containing no solvent. For example, it could have been a (partial?)
molec
Of
Anastassis Perrakis
Sent: Thursday, August 16, 2007 8:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools
1. Make the images available and demand a public apology for spoiling their
name.
2. Shut up, retract the paper, buy property in Alaska and
ht
> that it should be said.
>
> Cheers-
> Todd
>
>
> -Original Message-
> From: CCP4 bulletin board on behalf of Randy J. Read
> Sent: Thu 8/16/2007 8:22 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] The importance of USING our validation tools
>
PS I wasn't aware Nature now requires structure factors to be
submitted - which breaks down one of my arguments...
I still hope the authors provide the images though, otherwise I will
start suspecting much more structure than I do now.
In the meantime, all for required submission of raw images,
Hello All,
This debacle is actually quite reminiscent of a similar incident that Wayne
Hendrickson caught in
the 1970's concerning purported "tRNA crystals." Turned out to be completely
fabricated, and the
guy's career went down the drain, I think. A good example to tell your trainees.
Jacob Ke
On Thu, 16 Aug 2007, Kay Diederichs wrote:
Date: Thu, 16 Aug 2007 17:16:54 +0200
From: Kay Diederichs <[EMAIL PROTECTED]>
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools
I'm glad that the discussion has finally set in, and would o
The pdb will give the depositor the results of their validation runs and
identify problems - however they cannot force depositors to address those
problems...
J
Gina Clayton <[EMAIL PROTECTED]> wrote:>
> I thought that when a structure is deposited the databank does run its
> own
> refinement v
On Thu, Aug 16, 2007 at 03:13:29PM +0100, Phil Evans wrote:
> What do you count as raw data? Rawest are the images - everything
> beyond that is modellling - but archiving images is _expensive_!
Maybe we should contact Google to let them do it for us ;-)
http://news.bbc.co.uk/2/hi/technolog
I think the average structure is much less than 20 GB since most data
seems to be collected as SAD. I quickly looked at my data ~20
structures 3 MAD, 9 SAD, 3 MIR, 4 MR, number of amino acids per asu 150
- 9600, the average was closer to 3 GB (compressed). The largest dataset
24 GB (compressed
This structure (1h6w) provides an interesting comparison; it looks just
as I would expect though for such an interesting extended fold.
There are big peaks on the 3-fold axis; there is wispy density which
would be very hard to model - I found an ILE in the wrong rotamer (341A)
- (there is ALWAYS
Ashley Buckle wrote:
By raw data I mean images. We think this is only manageable using a
distributed data grid model (eg Universities/institutions setup their
own repositories using open standards, and PDB aggregate the links to
them. URL persistence will be a hurdle I admit).
This reminded
For nice crystals data processing is straightforward. For crystals with
large unit cells, high mosaicity, and diffuse scattering, processing
can be critical. It may be that future advances in integration
software will allow one to extract far better data from such a
diffraction dataset than can be
I'm glad that the discussion has finally set in, and would only like to
comment on the practicability of storing images.
Mischa Machius schrieb:
I don't think archiving images would be that expensive. For one, I have
found that most formats can be compressed quite substantially using
simple, s
Validation aside, access to raw data is also helpful for method
development (eg integration and scaling algorithms), on which we all
rely.
Ashley
On 17/08/2007, at 1:04 AM, Santarsiero, Bernard D. wrote:
Sorry, I think it's a waste of resources to store the raw images. I
think
we should tr
On Thu, Aug 16, 2007 at 03:13:29PM +0100, Phil Evans wrote:
> What do you count as raw data? Rawest are the images - everything
> beyond that is modellling - but archiving images is _expensive_!
Hmmm - not sure: let's say that a typical dataset requires about 180
images with 10Mb each image. W
On Aug 16, 2007, at 15:22, Randy J. Read wrote:
Raw images are probably even harder to simulate convincingly.
If i was to fabricate a structure, I would get first 'Fobs', then
expand, then get the images
(I am sure one can hack 'strategy' or 'predict' or even 'mosflm' to
tell you in which
Dear all,
With regards to the possible "fabrication" of the 2hr0 structure, why
would the authors have deposited the structure factors if this is not
required by the journal? Also, why would they have "fabricated" a
structure with gaps along c if they could have done so without the gap?
I
y email, but I just thought that it
should be said.
Cheers-
Todd
-Original Message-
From: CCP4 bulletin board on behalf of Randy J. Read
Sent: Thu 8/16/2007 8:22 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] The importance of USING our validation tools
On Aug 16 2007, Eleanor Do
Sorry, I think it's a waste of resources to store the raw images. I think
we should trust people to be able to at least process their own data set.
Besides, you would need to include beamline parameters, beam position,
detector distances, etc. that may or may not be correct in the image
headers. I'
Hmm - I think I miscalculated, by a factor of 100 even!... need more
coffee. In any case, I still think it would be doable. Best - MM
On Aug 16, 2007, at 9:30 AM, Mischa Machius wrote:
I don't think archiving images would be that expensive. For one, I
have found that most formats can be com
I don't think archiving images would be that expensive. For one, I
have found that most formats can be compressed quite substantially
using simple, standard procedures like bzip2. If optimized, raw
images won't take up that much space. Also, initially, only those
images that have been used
By raw data I mean images. We think this is only manageable using a
distributed data grid model (eg Universities/institutions setup their
own repositories using open standards, and PDB aggregate the links to
them. URL persistence will be a hurdle I admit). You are right in
that a single-rep
What do you count as raw data? Rawest are the images - everything
beyond that is modellling - but archiving images is _expensive_!
Unmerged intensities are probably more manageable
Phil
On 16 Aug 2007, at 15:05, Ashley Buckle wrote:
Dear Randy
These are very valid points, and I'm so gla
Dear Randy
These are very valid points, and I'm so glad you've taken the
important step of initiating this. For now I'd like to respond to one
of them, as it concerns something I and colleagues in Australia are
doing:
The more information that is available, the easier it will be to
dete
I believe that is so.
In this case the Rfactor against the deposited data is low. The question
to be addressed is whether the deposited data is of acceptable quality.
There are some poor distances but not many - the asymmetric unit is very
empty.
The Ramachandran plot is not good, and an autho
On Aug 16 2007, Eleanor Dodson wrote:
The weighting in REFMAC is a function of SigmA ( plotted in log file).
For this example it will be nearly 1 for all resolutions ranges so the
weights are pretty constant. There is also a contribution from the
"experimental" sigma, which in this case seems
I thought that when a structure is deposited the databank does run its own
refinement validation and geometry checks and gives you back what it finds i.e
distance problems etc and rfactor?
Quoting Eleanor Dodson <[EMAIL PROTECTED]>:
The weighting in REFMAC is a function of SigmA ( plotted in l
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