Re: [ccp4bb] Incorrect Structure in the PDB

[Tanner, John J.]

Relevant to this discussion, the 2018 ACA meeting in Toronto will have a 
session on

"Best practices for building, refining, and analyzing ligands in macromolecular 
structures”

co-chaired by Anna Gardberg and Kurt Krause.

I expect this session will include case studies of structures that went wrong 
as a way of educating the community about the potential pitfalls of building 
ligands into electron density.


John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A



On Jun 27, 2017, at 1:34 AM, Trevor Sewell 
> wrote:


I have come across a key paper in my field that describes an enzyme mechanism. 
Their work is based on a deposited structure – by other authors - that is 
incorrectly interpreted.

Is there a process for removing a demonstrably wrong structure (deposited by 
others) from the PDB and replacing it with a correctly interpreted structure 
based on the original data? Or is there an alternative, and generally 
recognized, way of getting the correct structure in the public domain?

Many thanks for your advice on this matter.

Trevor Sewell

Disclaimer - University of Cape Town This e-mail is subject to UCT policies and 
e-mail disclaimer published on our website at 
http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 
650 9111. If this e-mail is not related to the business of UCT, it is sent by 
the sender in an individual capacity. Please report security incidents or abuse 
via cs...@uct.ac.za

Re: [ccp4bb] Incorrect Structure in the PDB

[Tanner, John J.]

Trevor,

I can share our recent experience correcting the record about a misplaced 
ligand binding site. It represents one possible way to deal with erroneous 
structures.

Our analysis of structures of the proline biosynthetic enzyme PYCR1 deposited 
by another group in 2006 suggested that the NAD(P)H cofactor had been 
erroneously modeled into noise density, placing the ligand over 25 Angstrom 
from the canonical binding site for Rossmann fold enzymes. Because of our 
longstanding interest in proline metabolism, I felt compelled to set the record 
straight.  Therefore, we generated a clone, purified the protein, and 
determined several structures with different ligands bound. Sure enough, the 
ligands in the 2006 structures were incorrect.  The supplement to our paper 
includes a thorough analysis of the electron density of the incorrect 
structures (EDS maps, PDBREDO, and omit maps).  We also did kinetics and 
analytical ultracentrifugation studies.  In short, we did a fairly 
comprehensive biochemical and biophysical study of the enzyme.  Thus, pointing 
out someone else’s error was just one part of a larger paper.

http://faculty.missouri.edu/%7Etannerjj/tannergroup/pdfs/PYCR1JBC2017withSupp.pdf

https://www.ncbi.nlm.nih.gov/pubmed/28258219

Jack Tanner

John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A



On Jun 27, 2017, at 1:34 AM, Trevor Sewell 
> wrote:


I have come across a key paper in my field that describes an enzyme mechanism. 
Their work is based on a deposited structure – by other authors - that is 
incorrectly interpreted.

Is there a process for removing a demonstrably wrong structure (deposited by 
others) from the PDB and replacing it with a correctly interpreted structure 
based on the original data? Or is there an alternative, and generally 
recognized, way of getting the correct structure in the public domain?

Many thanks for your advice on this matter.

Trevor Sewell

Disclaimer - University of Cape Town This e-mail is subject to UCT policies and 
e-mail disclaimer published on our website at 
http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 
650 9111. If this e-mail is not related to the business of UCT, it is sent by 
the sender in an individual capacity. Please report security incidents or abuse 
via cs...@uct.ac.za

Re: [ccp4bb] Incorrect Structure in the PDB

[Tanner, John J.]

Trevor,

I can share our recent experience correcting the record about a misplaced 
ligand binding site. It represents one possible way to deal with erroneous 
structures.

Our analysis of structures of the proline biosynthetic enzyme PYCR1 deposited 
by another group in 2006 suggested that the NAD(P)H cofactor had been 
erroneously modeled into noise density, placing the ligand over 25 Angstrom 
from the canonical binding site for Rossmann fold enzymes. Because of our 
longstanding interest in proline metabolism, I felt compelled to set the record 
straight.  Therefore, we generated a clone, purified the protein, and 
determined several structures with different ligands bound. Sure enough, the 
ligands in the 2006 structures were incorrect.  The supplement to our paper 
includes a thorough analysis of the electron density of the incorrect 
structures (EDS maps, PDBREDO, and omit maps).  We also did kinetics and 
analytical ultracentrifugation studies.  In short, we did a fairly 
comprehensive biochemical and biophysical study of the enzyme.  Thus, pointing 
out someone else’s error was just one part of a larger paper.

http://faculty.missouri.edu/%7Etannerjj/tannergroup/pdfs/PYCR1JBC2017withSupp.pdf

https://www.ncbi.nlm.nih.gov/pubmed/28258219

Jack Tanner

John J. Tanner
Professor of Biochemistry and Chemistry
Chair, Biochemistry Department Graduate Admissions Committee
Department of Biochemistry
University of Missouri-Columbia
117 Schweitzer Hall
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-5635
Email: tanne...@missouri.edu
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html
Lab: Schlundt Annex rooms 3,6,9, 203B, 203C
Office: Schlundt Annex 203A



On Jun 27, 2017, at 1:34 AM, Trevor Sewell 
> wrote:


I have come across a key paper in my field that describes an enzyme mechanism. 
Their work is based on a deposited structure – by other authors - that is 
incorrectly interpreted.

Is there a process for removing a demonstrably wrong structure (deposited by 
others) from the PDB and replacing it with a correctly interpreted structure 
based on the original data? Or is there an alternative, and generally 
recognized, way of getting the correct structure in the public domain?

Many thanks for your advice on this matter.

Trevor Sewell

Disclaimer - University of Cape Town This e-mail is subject to UCT policies and 
e-mail disclaimer published on our website at 
http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 
650 9111. If this e-mail is not related to the business of UCT, it is sent by 
the sender in an individual capacity. Please report security incidents or abuse 
via cs...@uct.ac.za

Re: [ccp4bb] Incorrect Structure in the PDB

[Constance Jeffery]

Hi Trevor,

I think you should also email the authors of the key paper in your field that 
you mention.  They should be told that the structure they used to create the 
model of the mechanism was incorrectly interpreted and should have the 
opportunity to write a correction to their paper.

Best regards,
Connie Jeffery


> On Jun 27, 2017, at 2:34 AM, Trevor Sewell  wrote:
> 
>  
> I have come across a key paper in my field that describes an enzyme 
> mechanism. Their work is based on a deposited structure – by other authors - 
> that is incorrectly interpreted.
>  
> Is there a process for removing a demonstrably wrong structure (deposited by 
> others) from the PDB and replacing it with a correctly interpreted structure 
> based on the original data? Or is there an alternative, and generally 
> recognized, way of getting the correct structure in the public domain?
>  
> Many thanks for your advice on this matter.
>  
> Trevor Sewell
>  
> Disclaimer - University of Cape Town This e-mail is subject to UCT policies 
> and e-mail disclaimer published on our website at 
> http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 
> 21 650 9111. If this e-mail is not related to the business of UCT, it is sent 
> by the sender in an individual capacity. Please report security incidents or 
> abuse via cs...@uct.ac.za

Re: [ccp4bb] Incorrect Structure in the PDB

[Philippe BENAS]

I think the PDB (and Gerard DVD) got the answer with their quite new validation 
report provided for each entry.On the other hand PDBredo (Tassos & Co) is an 
excellent tool to compare a currently deposited structure and its reprocessed 
version (although it doesn't tell about the phasing).
Best,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : "Goldman, Adrian" <adrian.gold...@helsinki.fi>
 À : CCP4BB@JISCMAIL.AC.UK 
 Envoyé le : Mardi 27 juin 2017 10h59
 Objet : Re: [ccp4bb] Incorrect Structure in the PDB
   
I agree: I don’t think this is fraud, and was never even suggesting it.  If it 
were fraud, _I_ at least would back-transform my structure so that there 
weren’t horrible red and green blobs all over the place…!  I think it’s just 
sloppy - and the question remains, as posed by the original poster: what and 
how to do about the many examples?
Adrian


On 27 Jun 2017, at 11:55, Bernhard Rupp <hofkristall...@gmail.com> wrote:
I beg to differ. You are not pulling a murthy simply by depositing a poor or 
even wrong structure. Although the borderline beteeen sloppy work (and 
selfdeception) and reckless misleading of others can be floating, real cases of 
fraud and fabrication are almost exceptionally rare.
Best, br
On Jun 27, 2017 10:44, "Philippe BENAS" 
<0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:

Dear Adrian,
OK, I understand. You might be perfectly right. Moreover as I wrote it is 
difficult to tell something from a single mono view picture.And as you are 
pointing out their Ramachadran plots doe not look good at all. So they are poor 
crystallographers. But the question that remains is to know if their structure 
is really wron, I mean if the backbone is incorrect or not. For sure they might 
end up with a poor reputation as crystallographers if they publish so badly 
refined structures. But they might end up asKrishnaMurthy if the backbone of 
their published structures are wrong !

All the best,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau,Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails:philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



De : "Goldman, Adrian" <adrian.gold...@helsinki.fi>
À : Philippe BENAS <philippe_be...@yahoo.fr>
Envoyé le : Mardi 27 juin 2017 10h30
Objet : Re: [ccp4bb] Incorrect Structure in the PDB

Philippe
All I did was take their deposited mtz and coordinates.  The peak in question 
in green is about 7 sigma.  This structure (at 2 Å) has 3% 
ramanachandran-forbidden; one of their lower-resolution structures is 22%!  And 
no, given that the action of a fourier transform hasn’t changed, this is not 
the best structure that could have been built at that time (2002…).
Adrian

On 27 Jun 2017, at 11:22, Philippe BENAS <philippe_be...@yahoo.fr> wrote:
Dear Adrian, dear all, It does not look very clear to me that the side chain 
for this tyrosine is at a wrong place for instance (indeed Chi2 torsion angle 
could have multiple values = highly rotating aromatic ring). But it seems 
rather that the main chain is not correctly traced, which is probably worse. In 
addition it is difficult to tell something from just a mono view... This being 
said data collected by one group or another vary. For instance, resolution and 
hence R/free R can (generally) be improved. This does not imply that the 
structure coming from the lower resolution structure in wrong: it is just 
probably the best model that could have been built with the available data at 
that time.And on the contrary to other techniques we, crystallographers, have 
the chance of the Fourier transform which permits to have statistical 
indicators, such as R and free R, which give an indication about the accuracy 
of the reported structure. Similarly when solving the structure by experimental 
phasing we have also such indicator

Re: [ccp4bb] Incorrect Structure in the PDB

[Philippe BENAS]

Dear Bernhard,
I totally agree with you and it was absolutely the meaning of my first email 
while thinking the used F were coming from Adrian's data. And by the way of the 
second as well. This being said what about groups that publish always poor 
structures ? Ins't it in some way dishonest ?

Best,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : Bernhard Rupp <hofkristall...@gmail.com>
 À : Philippe BENAS <philippe_be...@yahoo.fr> 
Cc : "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@jiscmail.ac.uk>
 Envoyé le : Mardi 27 juin 2017 10h55
 Objet : Re: [ccp4bb] Incorrect Structure in the PDB
   
I beg to differ. You are not pulling a murthy simply by depositing a poor or 
even wrong structure. Although the borderline beteeen sloppy work (and 
selfdeception) and reckless misleading of others can be floating, real cases of 
fraud and fabrication are almost exceptionally rare.
Best, br
On Jun 27, 2017 10:44, "Philippe BENAS" 
<0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:

Dear Adrian,
OK, I understand. You might be perfectly right. Moreover as I wrote it is 
difficult to tell something from a single mono view picture.And as you are 
pointing out their Ramachadran plots doe not look good at all. So they are poor 
crystallographers. But the question that remains is to know if their structure 
is really wron, I mean if the backbone is incorrect or not. For sure they might 
end up with a poor reputation as crystallographers if they publish so badly 
refined structures. But they might end up as Krishna Murthy if the backbone of 
their published structures are wrong !

All the best,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.benas@parisdescartes. fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ- paris5.fr/ , http://lcrbw.pharmacie.univ- 
paris5.fr/spip.php?article18



  De : "Goldman, Adrian" <adrian.gold...@helsinki.fi>
 À : Philippe BENAS <philippe_be...@yahoo.fr> 
 Envoyé le : Mardi 27 juin 2017 10h30
 Objet : Re: [ccp4bb] Incorrect Structure in the PDB
   
Philippe
All I did was take their deposited mtz and coordinates.  The peak in question 
in green is about 7 sigma.  This structure (at 2 Å) has 3% 
ramanachandran-forbidden; one of their lower-resolution structures is 22%!  And 
no, given that the action of a fourier transform hasn’t changed, this is not 
the best structure that could have been built at that time (2002…).
Adrian

On 27 Jun 2017, at 11:22, Philippe BENAS <philippe_be...@yahoo.fr> wrote:
Dear Adrian, dear all, It does not look very clear to me that the side chain 
for this tyrosine is at a wrong place for instance (indeed Chi2 torsion angle 
could have multiple values = highly rotating aromatic ring). But it seems 
rather that the main chain is not correctly traced, which is probably worse. In 
addition it is difficult to tell something from just a mono view... This being 
said data collected by one group or another vary. For instance, resolution and 
hence R/free R can (generally) be improved. This does not imply that the 
structure coming from the lower resolution structure in wrong: it is just 
probably the best model that could have been built with the available data at 
that time.And on the contrary to other techniques we, crystallographers, have 
the chance of the Fourier transform which permits to have statistical 
indicators, such as R and free R, which give an indication about the accuracy 
of the reported structure. Similarly when solving the structure by experimental 
phasing we have also such indicators (e.g. the figure of merit, Rcullis, 
...).All these statistical factors (including those related to the collected 
I(hkl) themselves) allow to give more or less confidence to a deposited model. 
Now there are cases where people report a modelled part in their structure and 
this sounds fair to me as long as it is correctly stat

Re: [ccp4bb] Incorrect Structure in the PDB

[Goldman, Adrian]

I agree: I don’t think this is fraud, and was never even suggesting it.  If it 
were fraud, _I_ at least would back-transform my structure so that there 
weren’t horrible red and green blobs all over the place…!  I think it’s just 
sloppy - and the question remains, as posed by the original poster: what and 
how to do about the many examples?

Adrian


On 27 Jun 2017, at 11:55, Bernhard Rupp 
<hofkristall...@gmail.com<mailto:hofkristall...@gmail.com>> wrote:

I beg to differ. You are not pulling a murthy simply by depositing a poor or 
even wrong structure. Although the borderline beteeen sloppy work (and 
selfdeception) and reckless misleading of others can be floating, real cases of 
fraud and fabrication are almost exceptionally rare.

Best, br

On Jun 27, 2017 10:44, "Philippe BENAS" 
<0d88e888355a-dmarc-requ...@jiscmail.ac.uk<mailto:0d88e888355a-dmarc-requ...@jiscmail.ac.uk>>
 wrote:
Dear Adrian,

OK, I understand. You might be perfectly right. Moreover as I wrote it is 
difficult to tell something from a single mono view picture.
And as you are pointing out their Ramachadran plots doe not look good at all. 
So they are poor crystallographers. But the question that remains is to know if 
their structure is really wron, I mean if the backbone is incorrect or not. For 
sure they might end up with a poor reputation as crystallographers if they 
publish so badly refined structures. But they might end up as Krishna Murthy if 
the backbone of their published structures are wrong !

All the best,
Philippe


Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599<tel:+33%201%2053%2073%2015%2099>
E-mails: 
philippe.be...@parisdescartes.fr<mailto:philippe.be...@parisdescartes.fr>, 
philippe_be...@yahoo.fr<mailto:philippe_be...@yahoo.fr>
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18





De : "Goldman, Adrian" 
<adrian.gold...@helsinki.fi<mailto:adrian.gold...@helsinki.fi>>
À : Philippe BENAS <philippe_be...@yahoo.fr<mailto:philippe_be...@yahoo.fr>>
Envoyé le : Mardi 27 juin 2017 10h30

Objet : Re: [ccp4bb] Incorrect Structure in the PDB

Philippe

All I did was take their deposited mtz and coordinates.  The peak in question 
in green is about 7 sigma.  This structure (at 2 Å) has 3% 
ramanachandran-forbidden; one of their lower-resolution structures is 22%!  And 
no, given that the action of a fourier transform hasn’t changed, this is not 
the best structure that could have been built at that time (2002…).

Adrian

On 27 Jun 2017, at 11:22, Philippe BENAS 
<philippe_be...@yahoo.fr<mailto:philippe_be...@yahoo.fr>> wrote:

Dear Adrian, dear all,

It does not look very clear to me that the side chain for this tyrosine is at a 
wrong place for instance (indeed Chi2 torsion angle could have multiple values 
= highly rotating aromatic ring). But it seems rather that the main chain is 
not correctly traced, which is probably worse. In addition it is difficult to 
tell something from just a mono view...

This being said data collected by one group or another vary. For instance, 
resolution and hence R/free R can (generally) be improved. This does not imply 
that the structure coming from the lower resolution structure in wrong: it is 
just probably the best model that could have been built with the available data 
at that time.
And on the contrary to other techniques we, crystallographers, have the chance 
of the Fourier transform which permits to have statistical indicators, such as 
R and free R, which give an indication about the accuracy of the reported 
structure. Similarly when solving the structure by experimental phasing we have 
also such indicators (e.g. the figure of merit, Rcullis, ...).
All these statistical factors (including those related to the collected I(hkl) 
themselves) allow to give more or less confidence to a deposited model.

Now there are cases where people report a modelled part in their structure and 
this sounds fair to me as long as it is correctly stated in the publication and 
the PDB file.

Another scenario would be a poorly resolved, I mean with erroneous phases, and 
this is probably the most tricky case (too long to debate in this email)

And finally the last case corresponds to real scientific frauds such as the C. 
Murthy's case and that in principle end with multiple retractions, PDB 
withdrawals and a broken 

Re: [ccp4bb] Incorrect Structure in the PDB

[Bernhard Rupp]

I beg to differ. You are not pulling a murthy simply by depositing a poor
or even wrong structure. Although the borderline beteeen sloppy work (and
selfdeception) and reckless misleading of others can be floating, real
cases of fraud and fabrication are almost exceptionally rare.

Best, br

On Jun 27, 2017 10:44, "Philippe BENAS" <
0d88e888355a-dmarc-requ...@jiscmail.ac.uk> wrote:

Dear Adrian,

OK, I understand. You might be perfectly right. Moreover as I wrote it is
difficult to tell something from a single mono view picture.
And as you are pointing out their Ramachadran plots doe not look good at
all. So they are poor crystallographers. But the question that remains is
to know if their structure is really wron, I mean if the backbone is
incorrect or not. For sure they might end up with a poor reputation as
crystallographers if they publish so badly refined structures. But they
might end up as Krishna Murthy if the backbone of their published
structures are wrong !

All the best,
Philippe

--
Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui
glace le plaisir, - probablement comme un étranger tombant au milieu
d'enfants en train de danser une ronde", Alfred Delvau, Dictionnaire de la
langue verte (1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599 <+33%201%2053%2073%2015%2099>
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-
paris5.fr/spip.php?article18
--



--
*De :* "Goldman, Adrian" <adrian.gold...@helsinki.fi>
*À :* Philippe BENAS <philippe_be...@yahoo.fr>
*Envoyé le :* Mardi 27 juin 2017 10h30

*Objet :* Re: [ccp4bb] Incorrect Structure in the PDB

Philippe

All I did was take their deposited mtz and coordinates.  The peak in
question in green is about 7 sigma.  This structure (at 2 Å) has 3%
ramanachandran-forbidden; one of their lower-resolution structures is 22%!
And no, given that the action of a fourier transform hasn’t changed, this
is not the best structure that could have been built at that time (2002…).

Adrian

On 27 Jun 2017, at 11:22, Philippe BENAS <philippe_be...@yahoo.fr> wrote:

Dear Adrian, dear all,

It does not look very clear to me that the side chain for this tyrosine is
at a wrong place for instance (indeed Chi2 torsion angle could have
multiple values = highly rotating aromatic ring). But it seems rather that
the main chain is not correctly traced, which is probably worse. In
addition it is difficult to tell something from just a mono view...

This being said data collected by one group or another vary. For instance,
resolution and hence R/free R can (generally) be improved. This does not
imply that the structure coming from the lower resolution structure in
wrong: it is just probably the best model that could have been built with
the available data at that time.
And on the contrary to other techniques we, crystallographers, have the
chance of the Fourier transform which permits to have statistical
indicators, such as R and free R, which give an indication about the
accuracy of the reported structure. Similarly when solving the structure by
experimental phasing we have also such indicators (e.g. the figure of
merit, Rcullis, ...).
All these statistical factors (including those related to the collected
I(hkl) themselves) allow to give more or less confidence to a deposited
model.

Now there are cases where people report a modelled part in their structure
and this sounds fair to me as long as it is correctly stated in the
publication and the PDB file.

Another scenario would be a poorly resolved, I mean with erroneous phases,
and this is probably the most tricky case (too long to debate in this email)

And finally the last case corresponds to real scientific frauds such as the
C. Murthy's case and that in principle end with multiple retractions, PDB
withdrawals and a broken scientific career (even if take 15 years to get
the crook). And such structures must be reported to the PDB for sure !

Best regards,
Philippe

--
Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui
glace le plaisir, - probablement comme un étranger tombant au milieu
d'enfants en train de danser une ronde", Alfred Delvau, Dictionnaire de la
langue verte (1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599 <+33%201%2053%2073%2015%2099>
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie

Re: [ccp4bb] Incorrect Structure in the PDB

[Philippe BENAS]

Dear Adrian,
OK, I understand. You might be perfectly right. Moreover as I wrote it is 
difficult to tell something from a single mono view picture.And as you are 
pointing out their Ramachadran plots doe not look good at all. So they are poor 
crystallographers. But the question that remains is to know if their structure 
is really wron, I mean if the backbone is incorrect or not. For sure they might 
end up with a poor reputation as crystallographers if they publish so badly 
refined structures. But they might end up as Krishna Murthy if the backbone of 
their published structures are wrong !

All the best,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde", Alfred Delvau, Dictionnaire de la langue verte 
(1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



  De : "Goldman, Adrian" <adrian.gold...@helsinki.fi>
 À : Philippe BENAS <philippe_be...@yahoo.fr> 
 Envoyé le : Mardi 27 juin 2017 10h30
 Objet : Re: [ccp4bb] Incorrect Structure in the PDB
   
Philippe
All I did was take their deposited mtz and coordinates.  The peak in question 
in green is about 7 sigma.  This structure (at 2 Å) has 3% 
ramanachandran-forbidden; one of their lower-resolution structures is 22%!  And 
no, given that the action of a fourier transform hasn’t changed, this is not 
the best structure that could have been built at that time (2002…).
Adrian

On 27 Jun 2017, at 11:22, Philippe BENAS <philippe_be...@yahoo.fr> wrote:
Dear Adrian, dear all, It does not look very clear to me that the side chain 
for this tyrosine is at a wrong place for instance (indeed Chi2 torsion angle 
could have multiple values = highly rotating aromatic ring). But it seems 
rather that the main chain is not correctly traced, which is probably worse. In 
addition it is difficult to tell something from just a mono view... This being 
said data collected by one group or another vary. For instance, resolution and 
hence R/free R can (generally) be improved. This does not imply that the 
structure coming from the lower resolution structure in wrong: it is just 
probably the best model that could have been built with the available data at 
that time.And on the contrary to other techniques we, crystallographers, have 
the chance of the Fourier transform which permits to have statistical 
indicators, such as R and free R, which give an indication about the accuracy 
of the reported structure. Similarly when solving the structure by experimental 
phasing we have also such indicators (e.g. the figure of merit, Rcullis, 
...).All these statistical factors (including those related to the collected 
I(hkl) themselves) allow to give more or less confidence to a deposited model. 
Now there are cases where people report a modelled part in their structure and 
this sounds fair to me as long as it is correctly stated in the publication and 
the PDB file. Another scenario would be a poorly resolved, I mean with 
erroneous phases, and this is probably the most tricky case (too long to debate 
in this email)
And finally the last case corresponds to real scientific frauds such as the C. 
Murthy's case and that in principle end with multiple retractions, PDB 
withdrawals and a broken scientific career (even if take 15 years to get the 
crook). And such structures must be reported to the PDB for sure ! Best 
regards,Philippe Philippe BENAS, Ph.D.
Dog in the manger
"Un importun survient qui trouble l'intimité, qui arrête l'expansion, qui glace 
le plaisir, - probablement comme un étranger tombant au milieu d'enfants en 
train de danser une ronde",Alfred Delvau,Dictionnaire de la langue verte (1866).

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS
Faculté de Pharmacie, Université Paris Descartes
Case 48
Av, de l'Observatoire
F-75270 PARIS cedex 06
+33.1.5373.1599
E-mails:philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ 
,http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18



De : "Goldman, Adrian" <adrian.gold...@helsinki.fi>
À : CCP4BB@JISCMAIL.AC.UK 
Envoyé le : Mardi 27 juin 2017 9h36
Objet : Re: [ccp4bb] Incorrect Structure in the PDB

There are plenty of such structures in the PDB.  We have one that we are 
rerefining at the moment - and indeed there is a whole slew of structures from 
the same author, all done sloppily.  Here’s an example of a 2 Å (!) structure.  
The Tyr clearly goes into the green blob above it, and the loop conformation

Re: [ccp4bb] Incorrect Structure in the PDB

[Pietro Roversi]

On the subject of withdrawal of entries from the PDB, I just flag up another 
interesting aspect.

Four years ago I was Visiting Fellow in a colleague's lab, and in the course of 
the year I determined, refined and deposited 4 good structures, authored by me 
and my colleagues who were part of the research.

Due to a scientific disagreement on the manuscript describing the structures, 
my colleague wrote to the PDB and unilaterally withdrew the 4 entries, without 
letting me know in advance nor consulting me and against my will.

When I wrote to the PDB to complain (i was the depositor) they answered:

"Thank you for your email. According to the wwPDB policy, if there is a case of 
conflict between authors, the PI of the project makes the final decision. Since 
Dr.  is the PI for this project, we have to take his word as 
final. Please see below the extract of the policy 
(http://www.wwpdb.org/policy.html).

Please note, PDB cannot resolve any conflict between authors. This has to be 
resolved by the authors."

My colleague has since re-determined, re-refined and re-deposited the 
structures against the data taken from the crystals I grew (with his name as 
the only author of all 4 entries0 and they have published the work without 
granting me co-authorship on the paper. I wrote immediately to the journal and 
they suggested that the Institute where I carried out the research carry out an 
internal investigation. Which is ongoing.

It's all very well that all is done in good faith but sometimes on-trust policy 
+ absence of a "court" to appeal to in case of misconduct are a rather 
insufficient combination when it comes to PDB depositions/withdrawals.

with best wishes,

Pietro





best regards,
Sanchayita Sen
PDBe Depositions

Sent from my Desktop

Dr. Pietro Roversi
Oxford University Biochemistry Department - Glycobiology Division
South Parks Road
Oxford OX1 3QU England - UK
Tel. 0044 1865 275339

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Trevor Sewell 
[trevor.sew...@uct.ac.za]
Sent: 27 June 2017 07:34
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Incorrect Structure in the PDB


I have come across a key paper in my field that describes an enzyme mechanism. 
Their work is based on a deposited structure – by other authors - that is 
incorrectly interpreted.

Is there a process for removing a demonstrably wrong structure (deposited by 
others) from the PDB and replacing it with a correctly interpreted structure 
based on the original data? Or is there an alternative, and generally 
recognized, way of getting the correct structure in the public domain?

Many thanks for your advice on this matter.

Trevor Sewell

Disclaimer - University of Cape Town This e-mail is subject to UCT policies and 
e-mail disclaimer published on our website at 
http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 
650 9111. If this e-mail is not related to the business of UCT, it is sent by 
the sender in an individual capacity. Please report security incidents or abuse 
via cs...@uct.ac.za

Re: [ccp4bb] Incorrect Structure in the PDB

[Frank von Delft]

What tiny fraction of the gazillions it would cost to store all the raw 
data, would be enough to arrange the training courses needed to get the 
ballooning population of practitioners up to speed, he mused idly.



On 27/06/2017 09:21, Goldman, Adrian wrote:

That’s quite something.  To me, this thread raises another issue: I see a lot 
of comments about extracting the last little bit from every byte of data 
collected - but that’s not our main problem.  Our main problem appears to be 
shoddily-done refinement of data that are in fact perfectly decent (or decent 
enough that a quick browse in coot shows places that are horrendously wrong).  
Alwyn’s and Gerard’s article of 20 years ago or so “if freedom is given, 
liberties are taken” springs to mind.

Adrian

Re: [ccp4bb] Incorrect Structure in the PDB

[Goldman, Adrian]

That’s quite something.  To me, this thread raises another issue: I see a lot 
of comments about extracting the last little bit from every byte of data 
collected - but that’s not our main problem.  Our main problem appears to be 
shoddily-done refinement of data that are in fact perfectly decent (or decent 
enough that a quick browse in coot shows places that are horrendously wrong).  
Alwyn’s and Gerard’s article of 20 years ago or so “if freedom is given, 
liberties are taken” springs to mind.

Adrian

Re: [ccp4bb] Incorrect Structure in the PDB

[benjamin bax]

Hi Trevor,
  Some of my colleagues came across a misinterpreted structure published in 
Acta D., a couple of years ago.
They raised the issue with the editors of Acta D., who were most helpful in 
getting the issue sorted out.

My impression is that the journals are the responsible for the papers that they 
publish, and raising this type of issue with the journal editors initially - 
may be the best way forward.

Best regards, Ben 


On 27 Jun 2017, at 08:15, Trevor Sewell <trevor.sew...@uct.ac.za> wrote:

The misinterpretation is considerable I as can be seen from the attached coot 
screenshot.
 
I have no reason to suspect malfeasance. But it looks like the authors didn’t 
check very carefully.
I have re-interpreted and refined the density and it is just fine – Rfactor of 
18% for a 2.3A structure.
 
The critical reinterpretations concern  the orientation of the backbone near 
the active site and the interpretation of a blob of density claimed to be 
substrate in the original paper.
 
Maybe the best would be to write to the author and suggest that she obsolete 
the structure. We could see if we could  reach some agreement on how to take it 
further – perhaps a letter to the editor of JBC.
 
 
 
Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
 
From: Manfred S. Weiss <mailto:manfred.we...@helmholtz-berlin.de>
Sent: Tuesday, June 27, 2017 8:46 AM
To: Trevor Sewell <mailto:trevor.sew...@uct.ac.za>
Subject: Re: [ccp4bb] Incorrect Structure in the PDB
 
Dear Trevor,

you can download the incorrect structure and the associated data and 
reinterpret and
re-refine the structure. Then you can re-deposit provided you write a paper 
about the
new findings. This is currently the policy of the PDB.

Else, you can contact the authors of the incorrect structure and do the 
reinterpretation
together with them? They can replace the incorrect structure without a new 
publication.

That's all there is at the moment.

May I ask what is incorrect about the structure?

Cheers, 

Manfred

Am 27.06.2017 um 08:34 schrieb Trevor Sewell:
>  
> I have come across a key paper in my field that describes an enzyme 
> mechanism. Their work is based on a deposited structure – by other authors - 
> that is incorrectly interpreted.
>  
> Is there a process for removing a demonstrably wrong structure (deposited by 
> others) from the PDB and replacing it with a correctly interpreted structure 
> based on the original data? Or is there an alternative, and generally 
> recognized, way of getting the correct structure in the public domain? 
>  
> Many thanks for your advice on this matter.
>  
> Trevor Sewell
>  
> Disclaimer - University of Cape Town This e-mail is subject to UCT policies 
> and e-mail disclaimer published on our website 
> athttp://www.uct.ac.za/about/policies/emaildisclaimer/ 
> <https://protect-za.mimecast.com/s/vQqAB6SaJ5drIw> or obtainable from +27 21 
> 650 9111. If this e-mail is not related to the business of UCT, it is sent by 
> the sender in an individual capacity. Please report security incidents or 
> abuse via cs...@uct.ac.za <mailto:cs...@uct.ac.za>
-- 
Dr. Manfred S. Weiss
Macromolecular Crystallography
Helmholtz-Zentrum Berlin
Albert-Einstein-Str. 15
D-12489 Berlin
Germany


Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. 
Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de 
<https://protect-za.mimecast.com/s/ndaRBlf2pwDnU4>
Disclaimer - University of Cape Town This e-mail is subject to UCT policies and 
e-mail disclaimer published on our website at 
http://www.uct.ac.za/about/policies/emaildisclaimer/ 
<http://www.uct.ac.za/about/policies/emaildisclaimer/> or obtainable from +27 
21 650 9111. If this e-mail is not related to the business of UCT, it is sent 
by the sender in an individual capacity. Please report security incidents or 
abuse via cs...@uct.ac.za <mailto:cs...@uct.ac.za>


Dr Ben Bax

York Structural Biology Laboratory, 
Department of Chemistry, 
University of York,
York YO10 5DD

ben.d.v@gmail.com

 

 

Re: [ccp4bb] Incorrect Structure in the PDB

[Dale Tronrud]

   It can't hurt to try to work with the author, and it's the only way
to get the current PDB file out of the database.  If you don't get the
response you want you can still go ahead and look for a venue to publish
your own interpretation.

   Having a paper to go with the model is not only a requirement of the
wwPDB rules but it makes the situation much clearer the someone wanting
to understand this protein.  Having a second model in the PDB w/o a
publication would not leave many clues to decide which model to use.

Dale Tronrud

On 6/27/2017 12:15 AM, Trevor Sewell wrote:
> The misinterpretation is considerable I as can be seen from the attached
> coot screenshot.
> 
>  
> 
> I have no reason to suspect malfeasance. But it looks like the authors
> didn’t check very carefully.
> 
> I have re-interpreted and refined the density and it is just fine –
> Rfactor of 18% for a 2.3A structure.
> 
>  
> 
> The critical reinterpretations concern  the orientation of the backbone
> near the active site and the interpretation of a blob of density claimed
> to be substrate in the original paper.
> 
>  
> 
> Maybe the best would be to write to the author and suggest that she
> obsolete the structure. We could see if we could  reach some agreement
> on how to take it further – perhaps a letter to the editor of JBC.
> 
>  
> 
>  
> 
>  
> 
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
> 
>  
> 
> *From: *Manfred S. Weiss <mailto:manfred.we...@helmholtz-berlin.de>
> *Sent: *Tuesday, June 27, 2017 8:46 AM
> *To: *Trevor Sewell <mailto:trevor.sew...@uct.ac.za>
> *Subject: *Re: [ccp4bb] Incorrect Structure in the PDB
> 
>  
> 
> Dear Trevor,
> 
> you can download the incorrect structure and the associated data and
> reinterpret and
> re-refine the structure. Then you can re-deposit provided you write a
> paper about the
> new findings. This is currently the policy of the PDB.
> 
> Else, you can contact the authors of the incorrect structure and do the
> reinterpretation
> together with them? They can replace the incorrect structure without a
> new publication.
> 
> That's all there is at the moment.
> 
> May I ask what is incorrect about the structure?
> 
> Cheers,
> 
> Manfred
> 
> Am 27.06.2017 um 08:34 schrieb Trevor Sewell:
>>
>>  
>>
>> I have come across a key paper in my field that describes an enzyme
>> mechanism. Their work is based on a deposited structure – by other
>> authors - that is incorrectly interpreted.
>>
>>  
>>
>> Is there a process for removing a demonstrably wrong structure
>> (deposited by others) from the PDB and replacing it with a correctly
>> interpreted structure based on the original data? Or is there an
>> alternative, and generally recognized, way of getting the correct
>> structure in the public domain?
>>
>>  
>>
>> Many thanks for your advice on this matter.
>>
>>  
>>
>> Trevor Sewell
>>
>>  
>>
>> Disclaimer - University of Cape Town This e-mail is subject to UCT
>> policies and e-mail disclaimer published on our website at
>> http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable
>> from +27 21 650 9111. If this e-mail is not related to the business of
>> UCT, it is sent by the sender in an individual capacity. Please report
>> security incidents or abuse via cs...@uct.ac.za 
> 
> -- 
> Dr. Manfred S. Weiss
> Macromolecular Crystallography
> Helmholtz-Zentrum Berlin
> Albert-Einstein-Str. 15
> D-12489 Berlin
> Germany
> 
> 
> 
> 
> Helmholtz-Zentrum Berlin für Materialien und Energie GmbH
> 
> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher
> Forschungszentren e.V.
> 
> Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende
> Dr. Jutta Koch-Unterseher
> Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking
> 
> Sitz Berlin, AG Charlottenburg, 89 HRB 5583
> 
> Postadresse:
> Hahn-Meitner-Platz 1
> D-14109 Berlin
> 
> http://www.helmholtz-berlin.de
> <https://protect-za.mimecast.com/s/ndaRBlf2pwDnU4>
> Disclaimer - University of Cape Town This e-mail is subject to UCT
> policies and e-mail disclaimer published on our website at
> http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from
> +27 21 650 9111. If this e-mail is not related to the business of UCT,
> it is sent by the sender in an individual capacity. Please report
> security incidents or abuse via cs...@uct.ac.za

Re: [ccp4bb] Incorrect Structure in the PDB

[Tristan Croll]

Note that in most cases a structure may only be obsoleted with the written 
agreement of a senior author. From experience it's by far the best approach to 
work together with the original authors on a correction, in any case. Goodwill 
is an important thing.

If you wish, you can go it alone and deposit a new structure based on data from 
an existing deposition, but it won't obsolete the old structure and I believe 
it will only be accepted if accompanied by a peer-reviewed publication.

 Hope this helps,

Tristan
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

> On 27 Jun 2017, at 07:50, Vellieux Frédéric <frederic.velli...@ibt.cas.cz> 
> wrote:
> 
> Hello,
> 
> I think it makes sense to have a look at the policy of the PDB concerning 
> obsoleting structures:
> 
> The publication is retracted. The associated PDB entry will be obsoleted if 
> requested by the journal. If a request has not been received, the wwPDB will 
> do its best to contact the depositor and co-authors, (former) PIs, journal 
> editors, etc. when made aware of the retraction. If the reason(s) for 
> retraction were such that the associated PDB entry needs to be made obsolete, 
> the wwPDB will obsolete the entry. The citation in the obsoleted entry is the 
> published journal retraction.
> The structure is incorrect, and the entry author obsoletes the entry. The 
> entry must contain a statement as to the reason for obsoleting the structure.
> A third-party (such as the employer) requests that the entry is obsoleted 
> (e.g., in case of malfeasance). The citation in the obsoleted entry must be a 
> published explanation and retraction in a peer-reviewed journal.
>  
> Source: https://www.wwpdb.org/documentation/policy
> 
> Cheers,
> 
> Fred.
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Trevor 
> Sewell
> Sent: Tuesday, June 27, 2017 8:35 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Incorrect Structure in the PDB
>  
>  
> I have come across a key paper in my field that describes an enzyme 
> mechanism. Their work is based on a deposited structure – by other authors - 
> that is incorrectly interpreted.
>  
> Is there a process for removing a demonstrably wrong structure (deposited by 
> others) from the PDB and replacing it with a correctly interpreted structure 
> based on the original data? Or is there an alternative, and generally 
> recognized, way of getting the correct structure in the public domain?
>  
> Many thanks for your advice on this matter.
>  
> Trevor Sewell
>  
> Disclaimer - University of Cape Town This e-mail is subject to UCT policies 
> and e-mail disclaimer published on our website at 
> http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 
> 21 650 9111. If this e-mail is not related to the business of UCT, it is sent 
> by the sender in an individual capacity. Please report security incidents or 
> abuse via cs...@uct.ac.za
> - 
> Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato E-mailová 
> zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její 
> přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu 
> nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření 
> smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným 
> právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá 
> předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. 
> Disclaimer: If not expressly stated otherwise, this e-mail message (including 
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> Biotechnology CAS

Re: [ccp4bb] Incorrect Structure in the PDB

[Vellieux Frédéric]

Hello,

I think it makes sense to have a look at the policy of the PDB concerning 
obsoleting structures:

The publication is retracted. The associated PDB entry will be obsoleted if 
requested by the journal. If a request has not been received, the wwPDB will do 
its best to contact the depositor and co-authors, (former) PIs, journal 
editors, etc. when made aware of the retraction. If the reason(s) for 
retraction were such that the associated PDB entry needs to be made obsolete, 
the wwPDB will obsolete the entry. The citation in the obsoleted entry is the 
published journal retraction.
The structure is incorrect, and the entry author obsoletes the entry. The entry 
must contain a statement as to the reason for obsoleting the structure.
A third-party (such as the employer) requests that the entry is obsoleted 
(e.g., in case of malfeasance). The citation in the obsoleted entry must be a 
published explanation and retraction in a peer-reviewed journal.

Source: https://www.wwpdb.org/documentation/policy

Cheers,

Fred.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Trevor 
Sewell
Sent: Tuesday, June 27, 2017 8:35 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Incorrect Structure in the PDB


I have come across a key paper in my field that describes an enzyme mechanism. 
Their work is based on a deposited structure – by other authors - that is 
incorrectly interpreted.

Is there a process for removing a demonstrably wrong structure (deposited by 
others) from the PDB and replacing it with a correctly interpreted structure 
based on the original data? Or is there an alternative, and generally 
recognized, way of getting the correct structure in the public domain?

Many thanks for your advice on this matter.

Trevor Sewell

Disclaimer - University of Cape Town This e-mail is subject to UCT policies and 
e-mail disclaimer published on our website at 
http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 
650 9111. If this e-mail is not related to the business of UCT, it is sent by 
the sender in an individual capacity. Please report security incidents or abuse 
via cs...@uct.ac.za<mailto:cs...@uct.ac.za>
-

Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato E-mailová 
zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její 
přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu 
nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření 
smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním 
jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní 
odpovědnost Biotechnologického ústavu AV ČR, v. v. i.

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Biotechnology CAS

[ccp4bb] Incorrect Structure in the PDB

[Trevor Sewell]

I have come across a key paper in my field that describes an enzyme mechanism. 
Their work is based on a deposited structure – by other authors - that is 
incorrectly interpreted.

Is there a process for removing a demonstrably wrong structure (deposited by 
others) from the PDB and replacing it with a correctly interpreted structure 
based on the original data? Or is there an alternative, and generally 
recognized, way of getting the correct structure in the public domain?

Many thanks for your advice on this matter.

Trevor Sewell

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