Should we really have some crystallographers to review and qc those
structures before the formal releasing? JCSG has set a very good mechanism
for this issue.
There is a sever for self check.
http://smb.slac.stanford.edu/jcsg/QC/
On Thu, Aug 11, 2011 at 4:58 PM, Jacob Keller <
j-kell...@fsm
I think they fudged the data in this paper...
JPK
On Thu, Aug 11, 2011 at 6:30 PM, David Schuller wrote:
> link: http://iai.asm.org/cgi/reprint/IAI.05661-11v1
>
> Ferric C. Fang & Arturo Casadevall
> Retracted Science and the Retraction Index
> Infec. Immun. doi:10.1128/IAI.05661-11
>
> Abstract
link: http://iai.asm.org/cgi/reprint/IAI.05661-11v1
Ferric C. Fang & Arturo Casadevall
Retracted Science and the Retraction Index
Infec. Immun. doi:10.1128/IAI.05661-11
Abstract: Articles may be retracted when their findings are no longer
considered trustworthy due to scientific misconduct or e
I will second this. As an editor, i went through 8 referees - including all of
the authors' suggestions- to find just two. I was supposed to find three, but
we gave up at two.
Another, related point: I was at an iucr meeting a few years ago and complained
to Howard E, asking him why he was
> Some people on this list seem to think that reviewers are on the whole lazy
> and irresponsible and in need of some sort of public ridicule.
I hope it was not I who gave that impression by suggesting that some
of the blame go on the reviewers. Don't you think, indeed, that some
of the blame sho
Some people on this list seem to think that reviewers are on the whole lazy and
irresponsible and in need of some sort of public ridicule.
Please don't forget that reviewing manuscripts, while an important duty for
members of the community, is already in practice a completely thankless
voluntee
It's hard to blame the reviewers on this one. When I read the paper
I don't see anything to complain about other than the typo that swapped
the bond length and angle rmsd's and the insanely low average B factor.
If Table 1 had included the real stats for this model
bond length rmsd 0
Do reviewers ever get taken to task for these things? Don't they share
at least some of the responsibility? Maybe they should have to give
their explicit imprimatur, perhaps only after the fact, if published?
JPK
2011/8/11 Colin Nave :
> Well this article seems to have been refereed to 11 times
Yes, science is done by humans and mistakes will be made. Kudos
to the lab involved for owning up the mistake and doing the right
thing. It takes integrity to stand up in public and say "I screwed
up".
However, as a community of artisans we should not pass up the
opportunity to learn from
But, the mistakes in the retracted work could have been avoided easily if
the person did the structure spent some efforts to understand/know what
he/she is doing! or if the authors asked for some help from professionals.
Ibrahim
--
Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology
Well this article seems to have been refereed to 11 times so presumably these
11 publications also have to be retracted. I haven't checked the number of
citations for each of the 11 publications but articles citing these will also
be in doubt. And then ..
It reminds me somewhat of the Erdos
As the macromolecular crystallography becomes more automated and
user-friendly many biologists learn to solve structures and they can
make mistakes. Besides, new data become available that can give new
ideas etc. I don't think that's so horrible to make an honest mistake
and retract papers. Eve
Just another point - the macromolecular community are not the only ones with a
problem - I've just been shown
http://retractionwatch.wordpress.com/
which sheds some light on retractions. And also maybe says something about why
original data should be available/part of the review process.
J
___
Hi all,
Can someone confirm what exactly is the difference between the
"Wilson plot estimated B factor"
and the
"truncate style Wilson plot estimated B factor"
output by ctruncate?
Is it simply the difference between plotting the distribution of
I before and after the French+Wilson Bayesian c
Dale, This is exactly the conversation I just had with my student Jason,
right on!
The paper we are writing just now, this is figure 1.
But I always get rejected by Nature, so go figure.
On Thu, Aug 11, 2011 at 1:25 PM, Dale Tronrud wrote:
> I agree with Prof. Tomchick: if the point of your pap
I agree with Prof. Tomchick: if the point of your paper is your crystal
structure of
the binding of a ligand to a protein you should include a figure with the omit
map
(displayed without a "cover radius") that convinced you that binding took
place. I
prefer that map over some simulated, afte
On 11 Aug 2011, at 17:40, Diana Tomchick wrote:
> A quick glance at the header of the PDB file shows that there is one glaring
> discrepancy between it and the table in the paper that hasn't been mentioned
> yet in this forum. The data completeness (for data collection) reported in
> the paper
On Thu, Aug 11, 2011 at 9:40 AM, Diana Tomchick <
diana.tomch...@utsouthwestern.edu> wrote:
> A quick glance at the header of the PDB file shows that there is one
> glaring discrepancy between it and the table in the paper that hasn't been
> mentioned yet in this forum. The data completeness (for
A quick glance at the header of the PDB file shows that there is one glaring
discrepancy between it and the table in the paper that hasn't been mentioned
yet in this forum. The data completeness (for data collection) reported in the
paper is 95.7%, but in the header of the PDB file (actually, in
Hello,
Regarding your empty Tb site: How similar are the two copies of the protein in
the ASU? You can overlay the two individual copies from the ASU to check and
see if the binding site without density has been distorted somehow so that it
can no longer accomodate the Tb, maybe due to crystal
Hi Dale,
The data looks fine but the refinement for 3kj5, 2qns's 'improved' model, is
still pretty poor. Looking at the EDS maps for this entry there is some (model
bias) density for the ligand but, it is clearly not there. The PDB_REDO
optimization (http://www.cmbi.ru.nl/pdb_redo/kj/3kj5/index
And there's yet another one in today's Nature -- the paper hasn't been
retracted completely but the structural conclusions have:
http://www.nature.com/nature/journal/v476/n7359/full/nature10281.html
Corrigendum: Migrastatin analogues target fascin to block tumour metastasis
Again, the PDB entr
It is my understanding that there is no "retracted" category in the
wwPDB. Models are "obsoleted", usually with a replacement but sometimes
without. I don't know of a way to distinguish between those models obsoleted
for gross error and those simply replaced by one of higher quality. Surely
t
Hi Francis,
You may want to look into ACMI, which is designed for building into low
resolution maps.
In my experience with lower resolution data (4.2 - 4.5), "performing
well" is a different story than at higher resolutions. At low
resolution, I'd regard a composite omit map calculated fro
If you were to calculate the average B factor of the subset of atoms
in the protein that are exposed on the surface you would find that this
is higher as well. Most solvent atoms are on the surface of the molecule
and everything has higher mobility there.
I would be suspicious of a model wh
Message below...
Dear Nat,
I think this has actually been implemented, at least on the European side of
things. I've recently uploaded some structures to the PDB, via the EBI's
deposition service, and was given a link to the ePDB, with this very useful
information. Admittedly, I should have f
At the request of reviewers, I worked up the average B factor for some
structures using CCP4 programme BAVERAGE. Here's one example:
Protein33.1
Solvent53.9
Ligand32.9
I think the reviewer's question was directed at the quality of the model
for the ligand, but I notice that the ave
2011/8/11 Antony Oliver
> Surely in this ''modern age" data could be uploaded to "review server"
> whereby a reviewer could be given privileged access - to be able to see the
> model and maps, via something like AstexViewer, to gauge the quality and
> reliability of modelling - without actually g
Dear Frances, I think the answer is going to somewhat depend on whether you
need / want de-novo building, i.e straight from independent phases or if you
have a good quality homology model, that you can use as a "reference"
structure, or a good starting point.
"New" good things that are availab
Dear all
Does anybody have the list (pdb as well as structure factors) of all retracted
structures?
regards
Garib
On 10 Aug 2011, at 22:01, David Schuller wrote:
> Time to fuel up the gossip engines for the approaching weekend:
>
>
> http://www.sciencedirect.com/science/article/pii/S09692126
Hi ccp4bb'ers,
Of the automatic model builders out there (autobuild, arp/warp, buccaneer,
insert your own here), are there any opinions/personal experience on which of
these perform well in low resolution cases ( worse than say 3.5-3.8 ) ?
Thanks!
F
---
Surely in this ''modern age" data could be uploaded to "review server" whereby
a reviewer could be given privileged access - to be able to see the model and
maps, via something like AstexViewer, to gauge the quality and reliability of
modelling - without actually getting the PDB coordinates or s
sadaf iqbal wrote:
Hello everyone,
Do anybody know the correct procedure for calculating omit map in
CCP4, if one need to reduce the bias from the Molecular Replacement
structure. I am confused about the two options, one is fft map
calculation while the other is OMIT map calculation in Map &
Hello everyone,
Do anybody know the correct procedure for calculating omit map in CCP4, if one
need to reduce the bias from the Molecular Replacement structure. I am confused
about the two options, one is fft map calculation while the other is OMIT map
calculation in Map & Mask Utilities window
Perhaps paper and structure should be peer-reviewed independently, and only
when both have been given the green-light should both be released,
simultaneously.
I don't see why we should be especially precious about reviewing structural
data - we gladly hand functional data, protocols, etc to revie
Any structure deposited at the PDB should be peer-reviewed by a
crystallographer before acceptance by the PDB and his name should be
asociated to the pdb. This job cannot be done by the pdb team but a
crystallographer, not working in the field of the depositor to avoid
conflict, could detect er
What about going on a different route ? If the author name will be
confident as well it may cause the community to judge the scientific
part by itself without relating identities and locations. In that case
you may even allow the release of coordinates.
Another problem that may rise from deposit
On 11/08/11 09:13, Nian Huang wrote:
> To make my idea a little bit clearer, the reviewers first make the
> acceptance decision just based on the paper itself, on the condition the
> coordinate matches the description of the paper. Then the editor
> promises the publication date and the pdb can be
To make my idea a little bit clearer, the reviewers first make the
acceptance decision just based on the paper itself, on the condition the
coordinate matches the description of the paper. Then the editor promises
the publication date and the pdb can be subjected to final quick review,
either by th
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