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
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
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
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
Message - From: Jenny Martin
[EMAIL PROTECTED]
To: CCP4BB@JISCMAIL.AC.UK
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 the three is 1.9A
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against Jan Hendrik Schon (21 papers withdrawn, 15 in Science/Nature)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
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
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
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
- Original Message -
From: Jenny Martin [EMAIL PROTECTED]
To: CCP4BB@JISCMAIL.AC.UK
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
, 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 the three is 1.9A resolution with I/sigI 48
(top shell 2.5). My experience is that such crystals diffract very
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 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
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.
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 did not lead to a
successful
structure
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
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
-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 appeared
, 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 real measured data
and faked data. You just need
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
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,
. 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 resolutions ranges so
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 archiving images
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
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
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
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
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.
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
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
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
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
-
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 Dodson wrote:
The weighting in REFMAC is a function of SigmA
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
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
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.
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
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,
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
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
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 ;-)
don't ruffle anyones feathers by my 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
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
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?)
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
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
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
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
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
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 ATT as an
internet service provider. All the information will be automatically
copied and stored by the
50 matches
Mail list logo
