Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Better Beamline suggestion!

[CHAVAS Leonard]

Dear Chandra

SLS and ourselves (SOLEIL) are dealing rather often with large unit cells and 
fancy crystal orientations. No great secret, and things have already been 
mentioned: combining three-axis goniometry, large area Pixel detector, low 
background, small wedges and/or helical scans, Staraniso...

This works pretty well at SOLEIL, and I do know it works probably better at 
SLS. We can discuss off-line about more details if you wish.

Best.

leo

-
Leonard Chavas
- 
Synchrotron SOLEIL
Proxima-I
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
- 
Phone:  +33 169 359 746
Mobile: +33 644 321 614
E-mail: leonard.cha...@synchrotron-soleil.fr
-

> On 21 Aug 2019, at 21:47, Frank Von Delft  wrote:
> 
> We also described how to bend the loops in this article:  
> http://doi.org/gcb8j3  Figure 4 specifically.
> 
> 
> On 21/08/2019 18:21, Edwin Pozharski wrote:
>> 
>> In the absence of such you can resort to carefully bending the loop or 
>> bending the pin (Jim Holton made a nifty device for bending the pin) while 
>> keeping the xtal bathed in the cold stream.
>> 
>> 
>>  I would also mention these 
>> 
>> https://hamptonresearch.com/product-Adjustable-Mounted-CryoLoop-385.html
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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[ccp4bb] 3 years research assistant position for masters or junior postdocs

[Benini Stefano]

Dear All,

We have no internal candidates for the following position suitable either for a 
researcher with a MSc or a junior postdoc with experience in protein 
purification and possibly protein crystallization and crystallography.

The project:
Siderophore mediated iron uptake in Erwinia amylovora and Aspergillus 
fumigatus. Towards new strategies in plant and human health. (SupErA)
The project is in collaboration with Professor Hubertus Haas, Medical 
University Innsbruck, and Professor Sheref Mansy, University of Trento.

The project aims at the structural and functional characterization of proteins 
and enzymes involved in iron uptake in both the bacterial and fungal systems.

Links with information on how to apply are at the following links
https://www.unibz.it/en/home/position-calls/positions-for-academic-staff/4281-chimica-organica-dr-benini?group=18

call:
https://webservices.scientificnet.org/rest/uisdata/api/v1/tenders/attachments/43445

forms to apply:
https://webservices.scientificnet.org/rest/uisdata/api/v1/tenders/attachments/43446

Bolzano is located in the north of Italy at the border with Austria (2 hours 
train from Innsbruck Austria, 30' from Trento, Italy)

for informal enquiries (and scientific questions!) do not hesitate to contact me

some background information on one of the system to study could be found in 
this publication:
https://doi.org/10.1016/j.jsb.2018.02.002

deadline for application is 09/09/2019

have a nice day

S.

Stefano Benini, Ph.D. Assistant Professor
Guest editor of "Carbohydrate-Active Enzymes: Structure, Activity and Reaction 
Products"
A special issue of International Journal of Molecular 
Sciences (IF 4.183) (ISSN 1422-0067). This 
special issue belongs to the section "Molecular 
Biophysics". 
Deadline for manuscript submissions: 31 October 2019

https://www.mdpi.com/journal/ijms/special_issues/carbohydrate-active_enzymes


https://sbenini.people.unibz.it/
[https://s3.amazonaws.com/zapnito/uploads/f9805f649da7ceb38a2059ab1ce4f9bc/SciReports_EBM_Branded_Sig_v2.jpg]
https://www.unibz.it/en/faculties/sciencetechnology/academic-staff/person/27433-stefano-benini



"And money wasn't what I had in mind. Oh God, no, what I wanted was to do good. 
I was dying to do something good." Saul Bellow

"I don't like anything that's fake and I hate pretenders!" Stefano Benini
*
Bioorganic chemistry and Bio-Crystallography laboratory (B2Cl)
Faculty of Science and Technology
"Free" University of Bolzano
Piazza Università, 5
39100 Bolzano, Italy
Office (room K2.14):  +39 0471 017128
Laboratory (room E.021): +39 0471 017910
Fax: +39 0471 017009
https://sbenini.people.unibz.it/
orcid.org/-0001-6299-888X

"ogni giorno in più è un giorno in meno..."

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Stefano Benini, Ph.D. Assistant Professor
Guest editor of "Carbohydrate-Active Enzymes: Structure, Activity and Reaction 
Products"
A special issue of International Journal of Molecular 
Sciences (IF 4.183) (ISSN 1422-0067). This 
special issue belongs to the section "Molecular 
Biophysics". 
Deadline for manuscript submissions: 31 October 2019

https://www.mdpi.com/journal/ijms/special_issues/carbohydrate-active_enzymes


https://sbenini.people.unibz.it/
[https://s3.amazonaws.com/zapnito/uploads/f9805f649da7ceb38a2059ab1ce4f9bc/SciReports_EBM_Branded_Sig_v2.jpg]
https://www.unibz.it/en/faculties/sciencetechnology/academic-staff/person/27433-stefano-benini



"And money wasn't what I had in mind. Oh God, no, what I wanted was to do good. 
I was dying to do something good." Saul Bellow

"I don't like 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Better Beamline suggestion!

[Frank Von Delft]

We also described how to bend the loops in this article:  http://doi.org/gcb8j3 
 Figure 4 specifically.


On 21/08/2019 18:21, Edwin Pozharski wrote:

In the absence of such you can resort to carefully bending the loop or bending 
the pin (Jim Holton made a nifty device for bending the pin) while keeping the 
xtal bathed in the cold stream.


 I would also mention these

https://hamptonresearch.com/product-Adjustable-Mounted-CryoLoop-385.html



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[ccp4bb] Postdoc positions in Luca Lab at Moffitt Cancer Center

[Vince Luca]

Dear all,

Our laboratory (www.thelucalab.org) is recruiting postdoctoral researchers
interested in (1) studying the structural mechanisms of Notch receptor
activation and (2) designing biologics to control Notch activity on
specific tissue types. We use a multidisciplinary approach that integrates
structural and cellular biology with cutting edge protein engineering
techniques, such as directed evolution, to understand signaling mechanisms
at the molecular level. These projects incorporate both basic and
translational research, and Notch-targeted biologics will be evaluated as
potential therapies for autoimmunity, developmental disorders, and cancer.
Candidates will work with a team of immunologists, tumor biologists, and
clinicians at Moffitt Cancer Center (Tampa, FL) to conduct research in a
highly collaborative environment. The positions are funded for up to 5
years by an R35 MIRA grant from the NIH/NIGMS.

Ideal candidates have demonstrated expertise in protein biochemistry and
molecular biology. Expertise in x-ray crystallography and protein or
antibody engineering is preferred.

*Position highlights*
- Structure-function studies of Notch receptor signaling mechanisms
- Design biologics using protein engineering and directed evolution
- Collaboratively assess the therapeutic potential of biologics in disease
models

*Responsibilities*
- Protein purification, biophysical characterization of protein-protein
interactions, directed evolution, x-ray crystal structure determination,
cellular signaling assays
- Mentor graduate students and technicians
- Compose manuscripts and postdoctoral fellowships, assist with grant
applications

*Credentials and qualifications*
- PhD in Structural Biology, Molecular Biology, Biophysics, or a related
field (required)
- PhD awarded within the past year (preferred)

*How to apply*
Candidates should e-mail the following to vince.l...@moffitt.org:
1) A cover letter that describes their motivation to pursue this position
and summarizes past research accomplishments.
2) A current CV with recent publications and contact information for three
references.

*Moffitt Cancer Center Overview*
Moffitt Cancer and Research Institute is a rapidly expanding,
NCI-designated comprehensive cancer center that includes state of the art
core facilities to support basic research. The Moffitt Chemical Biology
Core is equipped with a Rigaku X-ray diffraction system and labs have
regular access to the Advanced Photon Source Synchrotron (SER-CAT
beamlines) for remote data collection. The Core also includes a Biacore
T200, Nanotemper MST, Microcal ITC for analyzing protein-protein
interactions and Mosquito crystallization robot for automated screening.
Moffitt Cancer Center is located within the coastal community of Tampa Bay
and is adjacent to the University of South Florida School of Medicine.

Best,
Vince

-- 
Vincent C. Luca, PhD.
Principal Investigator
Department of Drug Discovery
Moffitt Cancer Center & Research Institute
12902 USF Magnolia Dr
Tampa, FL 33612
www.thelucalab.org



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Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Better Beamline suggestion!

[Edwin Pozharski]

>
>
> In the absence of such you can resort to carefully bending the loop or
> bending the pin (Jim Holton made a nifty device for bending the pin) while
> keeping the xtal bathed in the cold stream.
>
>
 I would also mention these

https://hamptonresearch.com/product-Adjustable-Mounted-CryoLoop-385.html



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Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

[Jürgen Bosch]

I guess I should just reply with “B.” since you replied with A. :-)

More seriously, 

Both A & B will need to have real hard proof of their claims as this is a real 
mess in which they got themselves into.

It seems as A despite not been hired by B succeeded in getting another 
position, which is good. B has taken advantage of his/her power position by not 
hiring A. He/she will find excuses why A was not a good fit blabla. From a 
moral perspective B sucks.
Just imagine what A in B’s lab could have achieved by having someone in the 
project already knowing everything about the dubious protein with a four letter 
PDB code. Must be one of those Ego’s out there without true team leadership 
skills.

Regarding the IP, that’s more difficult and again will require written evidence 
unless a patent has been filed and then that should be relatively easy and have 
the lawyers go after it.

All of these actions require extra attention and mental resources - is it worth 
for A? If you just want to be right, then read on to the bottom of this email.

Is the publication in C formally correct? Other than that A claims B took 
his/her coordinates to solve the structure. All that really counts is that the 
science around PDB  is correct.

From my own experience during my postdoc time, we had a paper under review for 
nine months. I know who one of the reviewers was because he copy-protected his 
comments in the pdf - unfortunately for him on a Mac your login user account is 
added per default to the pdf as creator, and that was just his plain name. 
The day after his paper was accepted at a different journal, ours was finally 
accepted as well. It is remarkable how some figures in his paper just adopt the 
same orientation and show the same things as ours. I never followed up on this 
as it was not worth my time. I will not reveal the authors names but I’m sure 
smart pople like you can write a little perl script to query the PDB in a 
meaningful manner.

This was more than 2 cents I wanted to add to this discussion and hopefully A 
does see the value in my last paragraph.

Jürgen 


__
Jürgen Bosch, Ph.D.
Division of Pediatric Pulmonology and Allergy/Immunology
Case Western Reserve University
2109 Adelbert Rd, BRB 835
Cleveland, OH 44106
Phone: 216.368.7565
Fax: 216.368.4223
https://www.linkedin.com/in/jubosch/

CEO & Co-Founder at InterRayBio, LLC

Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology

> On Aug 21, 2019, at 4:49 AM, Anastassis Perrakis  wrote:
> 
> Something is unclear to me in the original question. What does “has used his 
> pdb for a publication” mean? Somebody used an entry already in the PDB? 
> Somebody used a “.pdb” coordinates file for publication (without “.mtz”)? 
> What was and is the relationship between A and B? 
> 
> In any case, assuming that A and B are not in talking terms (have you tried 
> through a mediator?), it is the director or designated ombudsperson of the 
> institute of A, that should review the case internally, and officially 
> contact the corresponding person of the institute of B. I can’t see what the 
> journal has to do with it, without a settlement between institutes. I also do 
> not consider a direct contact if A to the director of B appropriate. There 
> should be procedures for these cases. 
> 
> A. 
> 
> Sent from my iPhone
> 
> On 21 Aug 2019, at 10:12, Mark J van Raaij  > wrote:
> 
>> Dear Flemming,
>> 
>> As I understand it (I may be wrong), the final responsible institutions are 
>> those where the authors work. But as you say, they sometimes don't even 
>> reply - or they just may be very slow because they want to be really sure 
>> before committing to any answer.
>> 
>> But the journal has a responsibility also, to retract the paper if there is 
>> a serious suspicion the data were not obtained ethically. Of course, it may 
>> be difficult to prove ownership of a pdb file, if both authors claim 
>> ownership there is not really a way the journal can decide who is right. In 
>> my opinion, the journal should officially contact the institutions where the 
>> authors work to try and resolve this. The institutions may take the journal 
>> more seriously than a single researcher.
>> 
>> A generally respected institution that may advise on authorship disputes is 
>> COPE, Committee on Publication Ethics: https://publicationethics.org/ 
>> 
>> May also take a while though...
>> They have a database with anonymised examples of previously resolved 
>> disputes that may be helpful - you may find a similar situation on which 
>> they have "ruled". These are of course not legal rulings, but are considered 
>> by their members (most respectable journals) as a strong guideline.
>> This case may have similarities:
>> https://publicationethics.org/case/claim-stolen-data-and-demand-retractions 
>> 

Re: [ccp4bb] Problem in .mtz creation

[Vijayakumar Rajendran]

On Wed, 21 Aug 2019 at 19:35, Vijayakumar Rajendran <
vijayakumar.thenilgi...@gmail.com> wrote:

> Dear Eleanor,
> Thanks a lot. Its working great..
>
> On Wed, 21 Aug 2019 at 17:12, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Here is the reason!
>>
>>  Col SortMinMaxNum  % Mean Mean   Resolution
>> Type Column
>>  num order   Missing complete  abs.   LowHigh
>>   label
>>
>>1 ASC-80  80  0  100.00  0.3 30.2  61.16   1.00
>> H  H
>>2 NONE   -80  80  0  100.00  0.0 30.2  61.16   1.00
>> H  K
>>3 NONE 0  93  0  100.00 34.9 34.9  61.16   1.00
>> H  L
>>4 BOTH0.0 0.0 0  100.00 0.00 0.00  61.16   1.00
>> F  FCalc
>>5 NONE0.090.0 0  100.00 0.83 0.83  61.16   1.00
>> P  PHICalc
>>
>>
>>  No. of reflections used in FILE STATISTICS  1277880
>>
>> If your Fcalc range is 0.0 to 0.0 then there WILL be no density!
>> Not sure how you achieved that..
>>
>>
>> Oh yes I do..
>> Here are your coordinatesRYST1   80.620   80.620   93.880  90.00  90.00
>>  90.00 P 42 21 2 8
>> ORIGX1  1.00  0.00  0.000.0
>> ORIGX2  0.00  1.00  0.000.0
>> ORIGX3  0.00  0.00  1.000.0
>> SCALE1  0.012404  0.00  0.000.0
>> SCALE2  0.00  0.012404  0.000.0
>> SCALE3  0.00  0.00  0.0106520.0
>>   HETATM1  O   HOH A1001 -18.238  -1.176  25.716  0.00  0.00
>> O
>> HETATM2  O   HOH A1002 -18.238  -0.676  25.216  0.00  0.00
>> O
>> HETATM3  O   HOH A1003 -18.238  -0.676  25.716  0.00  0.00
>> O
>> HETATM4  O   HOH A1004 -18.238  -0.176  25.216  0.00  0.00
>> O
>> HETATM5  O   HOH A1005 -18.238  -0.176  25.716  0.00  0.00
>> O
>> HETATM6  O   HOH A1006 -17.738  -5.676  39.216  0.00  0.00
>> O
>> HETATM7  O   HOH A1007 -17.738  -5.176  39.216  0.00  0.00
>>
>>
>> Note all "atoms" have occupancy = 0.00...
>>
>> I have reset the occupancy to 1 and the Bvalue to 20 and now you get a
>> good looking map
>>
>> Here are new files
>> Eleanor
>>
>>
>>
>>
>> On Wed, 21 Aug 2019 at 09:12, Paul Emsley 
>> wrote:
>>
>>> On 20/08/2019 14:31, Vijayakumar Rajendran wrote:
>>>
>>> > I have a problem in viewing electron density map by opening .mtz file
>>> in coot. Actually I have a PDB
>>> > cordinates of water molecules of my protein using Hollow program. I
>>> generated the .mtz file using SFall
>>> > program in CCP4i by providing the cryst card. The generated mtz file
>>> contains FCalc and PhiCalc. When I open
>>> > this mtz file in coot along with the hollow pdb file, I am not getting
>>> the electron density.
>>>
>>> Why are you not getting electron density? What does Coot say in the
>>> terminal? Is there an error message on
>>> reading the mtz file? Is a map molecule generated? If so, what does the
>>> map density histogram look like?
>>>
>>> 
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>>
>
>
> --
>
> Dr. R. Vijayakumar,
> DBT- Research Associate,
> Molecular Biophysics Unit,
> Indian Institute of Science,
> Bangalore 560 012
> Website:  https://vijayphd.wixsite.com/home
> Research Gate: http://www.researchgate.net/profile/Vijayakumar_Rajendran
>


-- 

Dr. R. Vijayakumar,
DBT- Research Associate,
Molecular Biophysics Unit,
Indian Institute of Science,
Bangalore 560 012
Website:  https://vijayphd.wixsite.com/home
Research Gate: http://www.researchgate.net/profile/Vijayakumar_Rajendran



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[ccp4bb] 回复: [ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

[Flemming Goery]

I find the message in my original e-mail has changed, perhaps by hackers, and 
here I resend it as following:

Dear all:
A has sought a job in the lab of B. B invited A for a interview with a PPT oral 
presentation, as requested A has sent the PPT on the structural biology 
research of XXX to B by e-mail, and presented in front of B and his 
postdoctoral researcher.

After interview, B requested all research documents (including detailed 
reports, all done by A) on XXX to be sent by A to B by e-mail, A sent, 
including 2 sets of pdb for the same structure, one set with solvent, one 
without. A told B all intellectual property of the Documents and the research 
belonged to A, based on the regulation of A's institute.

B sought a referee from A's institute, to someone A did not agree. It seems the 
referee told B one set of PDB has been deposited (the one without solvent, also 
completed by A)

Then B did not give the offer to A. A joined Institute D, without independent 
funding for the writing (in fact, no salary to support this writing, and no fee 
for publication of this work).

Several years later, A found B's paper, i.e., the concerned paper published in 
Journal C. In the paper, B has used the information from deposited PDB for 9 
times (already a significant paprt of the paper, not to say the message from 
the other Documents sent to B by A). In the paper, it write something like, 
'based on our work on the structure of  (folowed by 4 letter pdb code)', which 
implied the structure was solved by the authors of the paper, rather than by A.

A contacted Journal C, Journal C contacted B, B claimed the deposited PDB was a 
public domain knowldge. Journal C took the action to add the reference to the 
deposited pdb in the paper.

As mentioned, the paper has mentioned and used the message from the deposited 
pdb 9 times, and in the paper the reference mark was not added to the first 
occurence of the mentioning of the deposited pdb, but added (only once in total 
for the 9 occurences of depositation code) to a paragraph where it can be 
concluded that the authors have used the undeposited pdb with the solvent. In 
another word, although reference to the deposited pdb was added by a 
correction, from where the reference mark was added, it cannot show they have 
refered to the cited pdb (completed by A), not to say the undeposited pdb with 
solvent which they used based on the paragraph information.

A's concern was that: A cannot exclude the possibility that the research in the 
paper other the part related to PDB, i.e., the part done in B's lab used in the 
paper, were fabricated by the current paper authors, thus A request paper 
retraction as the major claim.

If cannot retratcted, A request to be the correspondence author (sometimes 
requets co-first author, sometimes request both co-first author and 
co-correspondence author), as without A's work (the PPT presentation, 2 sets of 
pdb, all documents), the work in the concerned paper cannot be done. A regard 
as having contributed to the initiation of the paper, thus A prefer to be add 
as a co-correspondence author if appropriate.

First, can the paper deserve a retraction, and second, can A deserve a 
co-author?

Flemming


发件人: Nagarajan V 
发送时间: 2019年8月21日 21:17
收件人: Flemming Goery 
主题: Re: [ccp4bb] not solely pdb issue: need someone to officially settle the 
pdb dispute

Speaking somewhat from experience, C’s stance is more common. A can write to 
B’s funding agency or initiate action thru official channels to be acknowledged 
as a contributor. If successful, C will issue an addendum/erratum to this 
effect.

 V. Nagarajan

On Wed, Aug 21, 2019 at 2:13 AM Flemming Goery 
mailto:flemming_go...@hotmail.com>> wrote:
Dear all:
A has sought a job in the lab of B. B invited A for a interview with a PPT oral 
presentation, as requested B has sent the PPT on the structural biology 
research of XXX to B by e-mail, and presented in front of A and his 
postdoctoral researcher.

After interview, B requested all research documents (including detailed 
reports) on XXX to be sent by A to B by e-mail, A sent, including 2 sets of pdb 
for the same structure, one set with solvent, one without. A told B all 
intellectual property of the Documents and the research belonged to A, based on 
the regulation of A's institute.

B sought a referee from A's institute, to someone A did not agree. It seems the 
referee told B one set of PDB has been deposited (the one without solvent)

Then B did not give the offer to A. A joined Institute D, without independent 
funding for the writing (in fact, no salary to support this writing, and no fee 
for publication of this work).

Several years later, A found B's paper, i.e., the concerned paper published in 
Journal C. In the paper, B has used the information from deposited PDB for 9 
times (already a significant paprt of the paper, not to say the message from 
the other Documents sent to B by A). In 

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

[Herman . Schreuder]

Being denied a job because someone else published your research may make the 
dance also somewhat less happy…

Herman


Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Mark J 
van Raaij
Gesendet: Mittwoch, 21. August 2019 11:48
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] Re: [ccp4bb] not solely pdb issue: need someone to 
officially settle the pdb dispute


EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk

Another problem is that the structure was apparently originally not cited 
properly, and now still cited as work from the lab of B, rather than as work of 
A...

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616

On 21 Aug 2019, at 11:22, Anastassis Perrakis 
mailto:a.perra...@nki.nl>> wrote:

If the structure has been deposited in the PDB and thus is public ally 
available, B (or F, G, Φ, Ξ, Δ, Α or whoever else) has every right to use it in 
a publication.

“A” should follow the advice of Frank and do a happy dance for the usefulness 
of the work, or if not feeling like dancing she/he could follow my advice that 
will be offered in Greek: «ξυδάκι».
Sent from my iPhone

On 21 Aug 2019, at 11:13, Flemming Goery 
mailto:flemming_go...@hotmail.com>> wrote:
Dear all:
A has sought a job in the lab of B. B invited A for a interview with a PPT oral 
presentation, as requested B has sent the PPT on the structural biology 
research of XXX to B by e-mail, and presented in front of A and his 
postdoctoral researcher.

After interview, B requested all research documents (including detailed 
reports) on XXX to be sent by A to B by e-mail, A sent, including 2 sets of pdb 
for the same structure, one set with solvent, one without. A told B all 
intellectual property of the Documents and the research belonged to A, based on 
the regulation of A's institute.

B sought a referee from A's institute, to someone A did not agree. It seems the 
referee told B one set of PDB has been deposited (the one without solvent)

Then B did not give the offer to A. A joined Institute D, without independent 
funding for the writing (in fact, no salary to support this writing, and no fee 
for publication of this work).

Several years later, A found B's paper, i.e., the concerned paper published in 
Journal C. In the paper, B has used the information from deposited PDB for 9 
times (already a significant paprt of the paper, not to say the message from 
the other Documents sent to B by A). In the paper, it write something like, 
'based on our work on the structure of  (folowed by 4 letter pdb code)', which 
implied the structure was solved by the authors of the paper, rather than by A.

A contacted Journal C, Journal C contacted B, B claimed the deposited PDB was a 
public domain knowldge. Journal C took the action to add the reference to the 
deposited pdb in the paper.

As mentioned, the paper has mentioned and used the message from the deposited 
pdb 9 times, and in the paper the reference mark was not added to the first 
occurence of the mentioning of the deposited pdb, but added (only once for the 
9 occurences of depositation code) to a paragraph where it can be concluded 
that the authors have used the undeposited pdb with the solvent. In another 
words, although reference to the deposited pdb was added by a correction, from 
where the reference mark was added, it cannot show they have refered to the 
cited pdb, not to say the undeposited pdb with solvent which they used based on 
the paragraph information.

A's concern was that: A cannot exclude the possibility that the research in the 
paper other the part related to PDB, were fabricated, thus A request paper 
retraction as the major clain.

If cannot retratcted, A request to be the correspondence author (sometimes 
requets co-first author, sometimes request both co-first author and 
co-correspondence author), as without A's work (the PPT presentation, 2 sets of 
pdb, all documents), the work in the concerned paper cannot be done. A regard 
as having contributed to the initiation of the paper, thus A prefer to be add 
as a co-correspondence author if appropriate.

First, can the paper deserve a retraction, and second, can B deserve a 
co-author?

Flemming



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Re: [ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

[Mark J van Raaij]

Another problem is that the structure was apparently originally not cited 
properly, and now still cited as work from the lab of B, rather than as work of 
A...

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616


> On 21 Aug 2019, at 11:22, Anastassis Perrakis  wrote:
> 
> If the structure has been deposited in the PDB and thus is public ally 
> available, B (or F, G, Φ, Ξ, Δ, Α or whoever else) has every right to use it 
> in a publication. 
> 
> “A” should follow the advice of Frank and do a happy dance for the usefulness 
> of the work, or if not feeling like dancing she/he could follow my advice 
> that will be offered in Greek: «ξυδάκι». 
> 
> Sent from my iPhone
> 
> On 21 Aug 2019, at 11:13, Flemming Goery  > wrote:
> 
>> Dear all:
>> A has sought a job in the lab of B. B invited A for a interview with a PPT 
>> oral presentation, as requested B has sent the PPT on the structural biology 
>> research of XXX to B by e-mail, and presented in front of A and his 
>> postdoctoral researcher.
>> 
>> After interview, B requested all research documents (including detailed 
>> reports) on XXX to be sent by A to B by e-mail, A sent, including 2 sets of 
>> pdb for the same structure, one set with solvent, one without. A told B all 
>> intellectual property of the Documents and the research belonged to A, based 
>> on the regulation of A's institute.
>> 
>> B sought a referee from A's institute, to someone A did not agree. It seems 
>> the referee told B one set of PDB has been deposited (the one without 
>> solvent)
>> 
>> Then B did not give the offer to A. A joined Institute D, without 
>> independent funding for the writing (in fact, no salary to support this 
>> writing, and no fee for publication of this work).
>> 
>> Several years later, A found B's paper, i.e., the concerned paper published 
>> in Journal C. In the paper, B has used the information from deposited PDB 
>> for 9 times (already a significant paprt of the paper, not to say the 
>> message from the other Documents sent to B by A). In the paper, it write 
>> something like, 'based on our work on the structure of  (folowed by 4 letter 
>> pdb code)', which implied the structure was solved by the authors of the 
>> paper, rather than by A.
>> 
>> A contacted Journal C, Journal C contacted B, B claimed the deposited PDB 
>> was a public domain knowldge. Journal C took the action to add the reference 
>> to the deposited pdb in the paper.
>> 
>> As mentioned, the paper has mentioned and used the message from the 
>> deposited pdb 9 times, and in the paper the reference mark was not added to 
>> the first occurence of the mentioning of the deposited pdb, but added (only 
>> once for the 9 occurences of depositation code) to a paragraph where it can 
>> be concluded that the authors have used the undeposited pdb with the 
>> solvent. In another words, although reference to the deposited pdb was added 
>> by a correction, from where the reference mark was added, it cannot show 
>> they have refered to the cited pdb, not to say the undeposited pdb with 
>> solvent which they used based on the paragraph information.
>> 
>> A's concern was that: A cannot exclude the possibility that the research in 
>> the paper other the part related to PDB, were fabricated, thus A request 
>> paper retraction as the major clain.
>> 
>> If cannot retratcted, A request to be the correspondence author (sometimes 
>> requets co-first author, sometimes request both co-first author and 
>> co-correspondence author), as without A's work (the PPT presentation, 2 sets 
>> of pdb, all documents), the work in the concerned paper cannot be done. A 
>> regard as having contributed to the initiation of the paper, thus A prefer 
>> to be add as a co-correspondence author if appropriate.
>> 
>> First, can the paper deserve a retraction, and second, can B deserve a 
>> co-author?
>> 
>> Flemming
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
>> 
> To unsubscribe from the CCP4BB list, click the following link:
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> 



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Re: [ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

[Mark J van Raaij]

From the story, it seems to be a bit more complicated than that, using not only 
a deposited public-domain PDB, but also other data transferred confidentially 
(undeposited pdb and oral and written reports). This does seem unethical to me. 
I have to admit we only have one side of the story though.

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616


> On 21 Aug 2019, at 11:22, Anastassis Perrakis  wrote:
> 
> If the structure has been deposited in the PDB and thus is public ally 
> available, B (or F, G, Φ, Ξ, Δ, Α or whoever else) has every right to use it 
> in a publication. 
> 
> “A” should follow the advice of Frank and do a happy dance for the usefulness 
> of the work, or if not feeling like dancing she/he could follow my advice 
> that will be offered in Greek: «ξυδάκι». 
> 
> Sent from my iPhone
> 
> On 21 Aug 2019, at 11:13, Flemming Goery  > wrote:
> 
>> Dear all:
>> A has sought a job in the lab of B. B invited A for a interview with a PPT 
>> oral presentation, as requested B has sent the PPT on the structural biology 
>> research of XXX to B by e-mail, and presented in front of A and his 
>> postdoctoral researcher.
>> 
>> After interview, B requested all research documents (including detailed 
>> reports) on XXX to be sent by A to B by e-mail, A sent, including 2 sets of 
>> pdb for the same structure, one set with solvent, one without. A told B all 
>> intellectual property of the Documents and the research belonged to A, based 
>> on the regulation of A's institute.
>> 
>> B sought a referee from A's institute, to someone A did not agree. It seems 
>> the referee told B one set of PDB has been deposited (the one without 
>> solvent)
>> 
>> Then B did not give the offer to A. A joined Institute D, without 
>> independent funding for the writing (in fact, no salary to support this 
>> writing, and no fee for publication of this work).
>> 
>> Several years later, A found B's paper, i.e., the concerned paper published 
>> in Journal C. In the paper, B has used the information from deposited PDB 
>> for 9 times (already a significant paprt of the paper, not to say the 
>> message from the other Documents sent to B by A). In the paper, it write 
>> something like, 'based on our work on the structure of  (folowed by 4 letter 
>> pdb code)', which implied the structure was solved by the authors of the 
>> paper, rather than by A.
>> 
>> A contacted Journal C, Journal C contacted B, B claimed the deposited PDB 
>> was a public domain knowldge. Journal C took the action to add the reference 
>> to the deposited pdb in the paper.
>> 
>> As mentioned, the paper has mentioned and used the message from the 
>> deposited pdb 9 times, and in the paper the reference mark was not added to 
>> the first occurence of the mentioning of the deposited pdb, but added (only 
>> once for the 9 occurences of depositation code) to a paragraph where it can 
>> be concluded that the authors have used the undeposited pdb with the 
>> solvent. In another words, although reference to the deposited pdb was added 
>> by a correction, from where the reference mark was added, it cannot show 
>> they have refered to the cited pdb, not to say the undeposited pdb with 
>> solvent which they used based on the paragraph information.
>> 
>> A's concern was that: A cannot exclude the possibility that the research in 
>> the paper other the part related to PDB, were fabricated, thus A request 
>> paper retraction as the major clain.
>> 
>> If cannot retratcted, A request to be the correspondence author (sometimes 
>> requets co-first author, sometimes request both co-first author and 
>> co-correspondence author), as without A's work (the PPT presentation, 2 sets 
>> of pdb, all documents), the work in the concerned paper cannot be done. A 
>> regard as having contributed to the initiation of the paper, thus A prefer 
>> to be add as a co-correspondence author if appropriate.
>> 
>> First, can the paper deserve a retraction, and second, can B deserve a 
>> co-author?
>> 
>> Flemming
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
>> 
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Re: [ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

[Anastassis Perrakis]

If the structure has been deposited in the PDB and thus is public ally 
available, B (or F, G, Φ, Ξ, Δ, Α or whoever else) has every right to use it in 
a publication.

“A” should follow the advice of Frank and do a happy dance for the usefulness 
of the work, or if not feeling like dancing she/he could follow my advice that 
will be offered in Greek: «ξυδάκι».

Sent from my iPhone

On 21 Aug 2019, at 11:13, Flemming Goery 
mailto:flemming_go...@hotmail.com>> wrote:

Dear all:
A has sought a job in the lab of B. B invited A for a interview with a PPT oral 
presentation, as requested B has sent the PPT on the structural biology 
research of XXX to B by e-mail, and presented in front of A and his 
postdoctoral researcher.

After interview, B requested all research documents (including detailed 
reports) on XXX to be sent by A to B by e-mail, A sent, including 2 sets of pdb 
for the same structure, one set with solvent, one without. A told B all 
intellectual property of the Documents and the research belonged to A, based on 
the regulation of A's institute.

B sought a referee from A's institute, to someone A did not agree. It seems the 
referee told B one set of PDB has been deposited (the one without solvent)

Then B did not give the offer to A. A joined Institute D, without independent 
funding for the writing (in fact, no salary to support this writing, and no fee 
for publication of this work).

Several years later, A found B's paper, i.e., the concerned paper published in 
Journal C. In the paper, B has used the information from deposited PDB for 9 
times (already a significant paprt of the paper, not to say the message from 
the other Documents sent to B by A). In the paper, it write something like, 
'based on our work on the structure of  (folowed by 4 letter pdb code)', which 
implied the structure was solved by the authors of the paper, rather than by A.

A contacted Journal C, Journal C contacted B, B claimed the deposited PDB was a 
public domain knowldge. Journal C took the action to add the reference to the 
deposited pdb in the paper.

As mentioned, the paper has mentioned and used the message from the deposited 
pdb 9 times, and in the paper the reference mark was not added to the first 
occurence of the mentioning of the deposited pdb, but added (only once for the 
9 occurences of depositation code) to a paragraph where it can be concluded 
that the authors have used the undeposited pdb with the solvent. In another 
words, although reference to the deposited pdb was added by a correction, from 
where the reference mark was added, it cannot show they have refered to the 
cited pdb, not to say the undeposited pdb with solvent which they used based on 
the paragraph information.

A's concern was that: A cannot exclude the possibility that the research in the 
paper other the part related to PDB, were fabricated, thus A request paper 
retraction as the major clain.

If cannot retratcted, A request to be the correspondence author (sometimes 
requets co-first author, sometimes request both co-first author and 
co-correspondence author), as without A's work (the PPT presentation, 2 sets of 
pdb, all documents), the work in the concerned paper cannot be done. A regard 
as having contributed to the initiation of the paper, thus A prefer to be add 
as a co-correspondence author if appropriate.

First, can the paper deserve a retraction, and second, can B deserve a 
co-author?

Flemming




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Re: [ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

[Frank Von Delft]

If A had deposited it to the PDB immediately, he'd have had been able to claim 
the kudos and help lots of scientists besides B.

How is it that we structural biologists still are so precious about our 
coordinates?  Or more to the point, that the supervisors still don't teach 
their students that aggressive Open Access in all domains is where everything 
is going, and besides is ethically the correct way to think of what we do with 
the money society provides us with?


On 21/08/2019 10:13, Flemming Goery wrote:
Dear all:
A has sought a job in the lab of B. B invited A for a interview with a PPT oral 
presentation, as requested B has sent the PPT on the structural biology 
research of XXX to B by e-mail, and presented in front of A and his 
postdoctoral researcher.

After interview, B requested all research documents (including detailed 
reports) on XXX to be sent by A to B by e-mail, A sent, including 2 sets of pdb 
for the same structure, one set with solvent, one without. A told B all 
intellectual property of the Documents and the research belonged to A, based on 
the regulation of A's institute.

B sought a referee from A's institute, to someone A did not agree. It seems the 
referee told B one set of PDB has been deposited (the one without solvent)

Then B did not give the offer to A. A joined Institute D, without independent 
funding for the writing (in fact, no salary to support this writing, and no fee 
for publication of this work).

Several years later, A found B's paper, i.e., the concerned paper published in 
Journal C. In the paper, B has used the information from deposited PDB for 9 
times (already a significant paprt of the paper, not to say the message from 
the other Documents sent to B by A). In the paper, it write something like, 
'based on our work on the structure of  (folowed by 4 letter pdb code)', which 
implied the structure was solved by the authors of the paper, rather than by A.

A contacted Journal C, Journal C contacted B, B claimed the deposited PDB was a 
public domain knowldge. Journal C took the action to add the reference to the 
deposited pdb in the paper.

As mentioned, the paper has mentioned and used the message from the deposited 
pdb 9 times, and in the paper the reference mark was not added to the first 
occurence of the mentioning of the deposited pdb, but added (only once for the 
9 occurences of depositation code) to a paragraph where it can be concluded 
that the authors have used the undeposited pdb with the solvent. In another 
words, although reference to the deposited pdb was added by a correction, from 
where the reference mark was added, it cannot show they have refered to the 
cited pdb, not to say the undeposited pdb with solvent which they used based on 
the paragraph information.

A's concern was that: A cannot exclude the possibility that the research in the 
paper other the part related to PDB, were fabricated, thus A request paper 
retraction as the major clain.

If cannot retratcted, A request to be the correspondence author (sometimes 
requets co-first author, sometimes request both co-first author and 
co-correspondence author), as without A's work (the PPT presentation, 2 sets of 
pdb, all documents), the work in the concerned paper cannot be done. A regard 
as having contributed to the initiation of the paper, thus A prefer to be add 
as a co-correspondence author if appropriate.

First, can the paper deserve a retraction, and second, can B deserve a 
co-author?

Flemming




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[ccp4bb] not solely pdb issue: need someone to officially settle the pdb dispute

[Flemming Goery]

Dear all:
A has sought a job in the lab of B. B invited A for a interview with a PPT oral 
presentation, as requested B has sent the PPT on the structural biology 
research of XXX to B by e-mail, and presented in front of A and his 
postdoctoral researcher.

After interview, B requested all research documents (including detailed 
reports) on XXX to be sent by A to B by e-mail, A sent, including 2 sets of pdb 
for the same structure, one set with solvent, one without. A told B all 
intellectual property of the Documents and the research belonged to A, based on 
the regulation of A's institute.

B sought a referee from A's institute, to someone A did not agree. It seems the 
referee told B one set of PDB has been deposited (the one without solvent)

Then B did not give the offer to A. A joined Institute D, without independent 
funding for the writing (in fact, no salary to support this writing, and no fee 
for publication of this work).

Several years later, A found B's paper, i.e., the concerned paper published in 
Journal C. In the paper, B has used the information from deposited PDB for 9 
times (already a significant paprt of the paper, not to say the message from 
the other Documents sent to B by A). In the paper, it write something like, 
'based on our work on the structure of  (folowed by 4 letter pdb code)', which 
implied the structure was solved by the authors of the paper, rather than by A.

A contacted Journal C, Journal C contacted B, B claimed the deposited PDB was a 
public domain knowldge. Journal C took the action to add the reference to the 
deposited pdb in the paper.

As mentioned, the paper has mentioned and used the message from the deposited 
pdb 9 times, and in the paper the reference mark was not added to the first 
occurence of the mentioning of the deposited pdb, but added (only once for the 
9 occurences of depositation code) to a paragraph where it can be concluded 
that the authors have used the undeposited pdb with the solvent. In another 
words, although reference to the deposited pdb was added by a correction, from 
where the reference mark was added, it cannot show they have refered to the 
cited pdb, not to say the undeposited pdb with solvent which they used based on 
the paragraph information.

A's concern was that: A cannot exclude the possibility that the research in the 
paper other the part related to PDB, were fabricated, thus A request paper 
retraction as the major clain.

If cannot retratcted, A request to be the correspondence author (sometimes 
requets co-first author, sometimes request both co-first author and 
co-correspondence author), as without A's work (the PPT presentation, 2 sets of 
pdb, all documents), the work in the concerned paper cannot be done. A regard 
as having contributed to the initiation of the paper, thus A prefer to be add 
as a co-correspondence author if appropriate.

First, can the paper deserve a retraction, and second, can B deserve a 
co-author?

Flemming




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Re: [ccp4bb] AW: need someone officially settle a pdb dispute for a publication

[Frank Von Delft]

Structural genomics efforts have been putting PDBs in the public domain for 
almost 2 decades - precisely so they'd be used.  That's the whole point of the 
PDB, and open repositories:  set the data free, so it can make science happen.

"A" should be delighted that their work have actually been useful, and make a 
song and dance from the fact that science could move ahead unencumbered by 
their own (inevitable) inertia.  And even write a letter of congratulation to 
"B".  And stop spamming "C" so they can get on with evaluating the deluge of 
manuscripts.

phx


On 21/08/2019 08:54, 
herman.schreu...@sanofi.com wrote:
Dear Flemming,

As Jürgen said, what happened? Did A deposit the coordinate file in the pdb, 
but did not publish and did B take this coordinates and make a publication? Or 
did B ask A for the coordinates to have a look at and then made a publication 
without agreement of A? Did B hack the computer account of A and stole the 
coordinates?

In general, if a significant part of the publication of B were based on the 
coordinates produced by A, A should be coauthor. However, if the coordinates 
were deposited and A had ample time to write a publication, but did not do so, 
as Jürgen said, all A could ask for is to have his structure properly cited and 
acknowledged.

Something about tactics: Institute heads tend to protect their own people, so 
if the head of institute B gets an email from someone he/she does not know 
complaining about one of the people of his/hers institute, the institute head 
may not find the time to go through the trouble of a misconduct investigation 
with may harm the reputation of the institute.

However, if the head of institute A would learn that one of its people has been 
plagiarized by someone of institute B, the motivation to react will be much 
higher, especially if institute A and B are in a friendly competition.

So if I were A, I would go the head of institute A and complain about the 
academic misconduct of B and discuss what steps could be taken.

My 2 cents,
Herman



Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Flemming 
Goery
Gesendet: Dienstag, 20. August 2019 17:46
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] need someone officially settle a pdb dispute for a 
publication


EXTERNAL : Real sender is 
owner-ccp...@jiscmail.ac.uk

Dear All,

A and B belong to 2 different institutes. A claimed B has used his pdb for a 
publication in Journal C. Journal C did not give the retraction, but permit 
complain related to the journal publication author issue, with the prerequisite 
journal C did not have the authority on authorship dispute. Then A has e-mailed 
to the institute head of B with academic misconduct by B as claim, the 
institute head of B did not give reply.

In this situation, can A have the journal  authorship  dispute settled by a 
neutral reviewer (Journal C view: you (A) need to reach out to the institutions 
that have authority to adjudicate on such matters, as investigation and 
adjudication on authorship claims falls outside the remit of journal editors. 
)? Who are qualified as the neutral reviewer so that the review decision can be 
submitted to Journal C?

If you believe you are qualified, or you know somebody or some organization 
qualified, please let me know and I will introduce the issue to you by separate 
e-mail (it is best not disseminated, am I right?)

Best regards.

Flemming




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Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

[Anastassis Perrakis]

Something is unclear to me in the original question. What does “has used his 
pdb for a publication” mean? Somebody used an entry already in the PDB? 
Somebody used a “.pdb” coordinates file for publication (without “.mtz”)? What 
was and is the relationship between A and B?

In any case, assuming that A and B are not in talking terms (have you tried 
through a mediator?), it is the director or designated ombudsperson of the 
institute of A, that should review the case internally, and officially contact 
the corresponding person of the institute of B. I can’t see what the journal 
has to do with it, without a settlement between institutes. I also do not 
consider a direct contact if A to the director of B appropriate. There should 
be procedures for these cases.

A.

Sent from my iPhone

On 21 Aug 2019, at 10:12, Mark J van Raaij 
mailto:mjvanra...@cnb.csic.es>> wrote:

Dear Flemming,

As I understand it (I may be wrong), the final responsible institutions are 
those where the authors work. But as you say, they sometimes don't even reply - 
or they just may be very slow because they want to be really sure before 
committing to any answer.

But the journal has a responsibility also, to retract the paper if there is a 
serious suspicion the data were not obtained ethically. Of course, it may be 
difficult to prove ownership of a pdb file, if both authors claim ownership 
there is not really a way the journal can decide who is right. In my opinion, 
the journal should officially contact the institutions where the authors work 
to try and resolve this. The institutions may take the journal more seriously 
than a single researcher.

A generally respected institution that may advise on authorship disputes is 
COPE, Committee on Publication Ethics: https://publicationethics.org/
May also take a while though...
They have a database with anonymised examples of previously resolved disputes 
that may be helpful - you may find a similar situation on which they have 
"ruled". These are of course not legal rulings, but are considered by their 
members (most respectable journals) as a strong guideline.
This case may have similarities:
https://publicationethics.org/case/claim-stolen-data-and-demand-retractions

Best of luck,

Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616


On 20 Aug 2019, at 17:45, Flemming Goery 
mailto:flemming_go...@hotmail.com>> wrote:

Dear All,

A and B belong to 2 different institutes. A claimed B has used his pdb for a 
publication in Journal C. Journal C did not give the retraction, but permit 
complain related to the journal publication author issue, with the prerequisite 
journal C did not have the authority on authorship dispute. Then A has e-mailed 
to the institute head of B with academic misconduct by B as claim, the 
institute head of B did not give reply.

In this situation, can A have the journal  authorship  dispute settled by a 
neutral reviewer (Journal C view: you (A) need to reach out to the institutions 
that have authority to adjudicate on such matters, as investigation and 
adjudication on authorship claims falls outside the remit of journal editors. 
)? Who are qualified as the neutral reviewer so that the review decision can be 
submitted to Journal C?

If you believe you are qualified, or you know somebody or some organization 
qualified, please let me know and I will introduce the issue to you by separate 
e-mail (it is best not disseminated, am I right?)

Best regards.

Flemming



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Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

[Coker, Alun]

Dear Flemming,

This would be an intellectual property dispute. A is cleaning that B has used 
his IP without agreement. Most universities (and I assume other organisations) 
have IP policies that protect staff from having there IP stolen; the IP 
nominally belongs to the institution so the theft is legally from A's 
institution. I suggest that the correct procedure would be for A to contact 
their department responsible for IP to pursue B for IP theft.

Universities are highly sensitive to reputational damage so B's institution are 
likely not to back B if there is a reputational risk. Theft of IP would 
constitute a high risk of reputational damage.

All the best,

Alun

Dr Alun R. Coker
Associate Professor
University College London Division of Medicine
The Rayne Building
5 University Street
London
WC1E 6JF

Tel: 020 7679 6703 Ext 46703
Web: www.ucl.ac.uk/pxmed




From: Mark J van Raaij
Sent: Wednesday 21 August, 09:12
Subject: Re: [ccp4bb] need someone officially settle a pdb dispute for a 
publication
To: CCP4BB@JISCMAIL.AC.UK


Dear Flemming,

As I understand it (I may be wrong), the final responsible institutions are 
those where the authors work. But as you say, they sometimes don't even reply - 
or they just may be very slow because they want to be really sure before 
committing to any answer.

But the journal has a responsibility also, to retract the paper if there is a 
serious suspicion the data were not obtained ethically. Of course, it may be 
difficult to prove ownership of a pdb file, if both authors claim ownership 
there is not really a way the journal can decide who is right. In my opinion, 
the journal should officially contact the institutions where the authors work 
to try and resolve this. The institutions may take the journal more seriously 
than a single researcher.

A generally respected institution that may advise on authorship disputes is 
COPE, Committee on Publication Ethics: 
https://publicationethics.org/
May also take a while though...
They have a database with anonymised examples of previously resolved disputes 
that may be helpful - you may find a similar situation on which they have 
"ruled". These are of course not legal rulings, but are considered by their 
members (most respectable journals) as a strong guideline.
This case may have similarities:
https://publicationethics.org/case/claim-stolen-data-and-demand-retractions

Best of luck,

Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616


On 20 Aug 2019, at 17:45, Flemming Goery 
mailto:flemming_go...@hotmail.com>> wrote:

Dear All,

A and B belong to 2 different institutes. A claimed B has used his pdb for a 
publication in Journal C. Journal C did not give the retraction, but permit 
complain related to the journal publication author issue, with the prerequisite 
journal C did not have the authority on authorship dispute. Then A has e-mailed 
to the institute head of B with academic misconduct by B as claim, the 
institute head of B did not give reply.

In this situation, can A have the journal  authorship  dispute settled by a 
neutral reviewer (Journal C view: you (A) need to reach out to the institutions 
that have authority to adjudicate on such matters, as investigation and 
adjudication on authorship claims falls outside the remit of journal editors. 
)? Who are qualified as the neutral reviewer so that the review decision can be 
submitted to Journal C?

If you believe you are qualified, or you know somebody or some organization 
qualified, please let me know and I will introduce the issue to you by separate 
e-mail (it is best not disseminated, am I right?)

Best regards.

Flemming


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Re: [ccp4bb] Problem in .mtz creation

[Paul Emsley]

On 20/08/2019 14:31, Vijayakumar Rajendran wrote:

I have a problem in viewing electron density map by opening .mtz file in coot. Actually I have a PDB 
cordinates of water molecules of my protein using Hollow program. I generated the .mtz file using SFall 
program in CCP4i by providing the cryst card. The generated mtz file contains FCalc and PhiCalc. When I open 
this mtz file in coot along with the hollow pdb file, I am not getting the electron density.


Why are you not getting electron density? What does Coot say in the terminal? Is there an error message on 
reading the mtz file? Is a map molecule generated? If so, what does the map density histogram look like?




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Re: [ccp4bb] need someone officially settle a pdb dispute for a publication

[Mark J van Raaij]

Dear Flemming,

As I understand it (I may be wrong), the final responsible institutions are 
those where the authors work. But as you say, they sometimes don't even reply - 
or they just may be very slow because they want to be really sure before 
committing to any answer.

But the journal has a responsibility also, to retract the paper if there is a 
serious suspicion the data were not obtained ethically. Of course, it may be 
difficult to prove ownership of a pdb file, if both authors claim ownership 
there is not really a way the journal can decide who is right. In my opinion, 
the journal should officially contact the institutions where the authors work 
to try and resolve this. The institutions may take the journal more seriously 
than a single researcher.

A generally respected institution that may advise on authorship disputes is 
COPE, Committee on Publication Ethics: https://publicationethics.org/ 

May also take a while though...
They have a database with anonymised examples of previously resolved disputes 
that may be helpful - you may find a similar situation on which they have 
"ruled". These are of course not legal rulings, but are considered by their 
members (most respectable journals) as a strong guideline.
This case may have similarities:
https://publicationethics.org/case/claim-stolen-data-and-demand-retractions 


Best of luck,

Mark

Mark J van Raaij
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
calle Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616


> On 20 Aug 2019, at 17:45, Flemming Goery  wrote:
> 
> Dear All, 
> 
> A and B belong to 2 different institutes. A claimed B has used his pdb for a 
> publication in Journal C. Journal C did not give the retraction, but permit 
> complain related to the journal publication author issue, with the 
> prerequisite journal C did not have the authority on authorship dispute. Then 
> A has e-mailed to the institute head of B with academic misconduct by B as 
> claim, the institute head of B did not give reply.
> 
> In this situation, can A have the journal  authorship  dispute settled by a 
> neutral reviewer (Journal C view: you (A) need to reach out to the 
> institutions that have authority to adjudicate on such matters, as 
> investigation and adjudication on authorship claims falls outside the remit 
> of journal editors. )? Who are qualified as the neutral reviewer so that the 
> review decision can be submitted to Journal C?
> 
> If you believe you are qualified, or you know somebody or some organization 
> qualified, please let me know and I will introduce the issue to you by 
> separate e-mail (it is best not disseminated, am I right?)
> 
> Best regards.
> 
> Flemming
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 
> 



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[ccp4bb] AW: need someone officially settle a pdb dispute for a publication

[Herman . Schreuder]

Dear Flemming,

As Jürgen said, what happened? Did A deposit the coordinate file in the pdb, 
but did not publish and did B take this coordinates and make a publication? Or 
did B ask A for the coordinates to have a look at and then made a publication 
without agreement of A? Did B hack the computer account of A and stole the 
coordinates?

In general, if a significant part of the publication of B were based on the 
coordinates produced by A, A should be coauthor. However, if the coordinates 
were deposited and A had ample time to write a publication, but did not do so, 
as Jürgen said, all A could ask for is to have his structure properly cited and 
acknowledged.

Something about tactics: Institute heads tend to protect their own people, so 
if the head of institute B gets an email from someone he/she does not know 
complaining about one of the people of his/hers institute, the institute head 
may not find the time to go through the trouble of a misconduct investigation 
with may harm the reputation of the institute.

However, if the head of institute A would learn that one of its people has been 
plagiarized by someone of institute B, the motivation to react will be much 
higher, especially if institute A and B are in a friendly competition.

So if I were A, I would go the head of institute A and complain about the 
academic misconduct of B and discuss what steps could be taken.

My 2 cents,
Herman



Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Flemming 
Goery
Gesendet: Dienstag, 20. August 2019 17:46
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] need someone officially settle a pdb dispute for a 
publication


EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk

Dear All,

A and B belong to 2 different institutes. A claimed B has used his pdb for a 
publication in Journal C. Journal C did not give the retraction, but permit 
complain related to the journal publication author issue, with the prerequisite 
journal C did not have the authority on authorship dispute. Then A has e-mailed 
to the institute head of B with academic misconduct by B as claim, the 
institute head of B did not give reply.

In this situation, can A have the journal  authorship  dispute settled by a 
neutral reviewer (Journal C view: you (A) need to reach out to the institutions 
that have authority to adjudicate on such matters, as investigation and 
adjudication on authorship claims falls outside the remit of journal editors. 
)? Who are qualified as the neutral reviewer so that the review decision can be 
submitted to Journal C?

If you believe you are qualified, or you know somebody or some organization 
qualified, please let me know and I will introduce the issue to you by separate 
e-mail (it is best not disseminated, am I right?)

Best regards.

Flemming




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1



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Re: [ccp4bb] Problem in real space - please sign & invite other scientists to sign this letter

[David Briggs]

Dear Daniel,

I could not disagree with you more. As scientists it falls to us to support our 
colleagues (from whatever other discipline) when they provide evidence that has 
profound ramifications for humanity.

Would we hesitate to stand by colleagues who (for example) demonstrate the 
efficacy of vaccination, or that the earth really is an oblate spheroid?

If me being a signatory (not author, important distinction, as noted above) to 
this helps get this message across in even a small way, then it is 2 minutes of 
my time well spent.

As for whether or not scientists from one discipline can make a valuable and 
informed contributions to another, I hope Kevin Cowtan won't mind that I 
suggest you take a look at his work on climate modelling.

Dave

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs



From: Edwin Pozharski
Sent: Wednesday, August 21, 06:34
Subject: Re: [ccp4bb] Problem in real space - please sign & invite other 
scientists to sign this letter
To: CCP4BB@JISCMAIL.AC.UK


Dear Daniel,

with all due respect, I do believe that you are making several mistakes in your 
argument.

English is not my native tongue, but I suspect that there is a substantial 
difference between "author" and "signatory".  What people are asked to do here 
is essentially to sign a petition, not to become a co-author in traditional 
sense.  There were 39 signatories to the US Constitution, certainly not all of 
them are considered its authors.

Furthermore, most structural biologists are trained scientists and it is rather 
routine part of our job to evaluate research we are not exactly experts in.  I 
am not a climatologist, but I do take exception to your assertion that I am 
therefore automatically too ignorant to understand basic concepts that pertain 
to global warming and climate change.  A climatologist wouldn't instantly know 
what B-factors are, but is certainly capable of understanding the concept if 
you explain it.

Using physical science and its data to arrive at conclusions regarding 
religion, politics and economic theory (!) is not at all embarrassing.  (And 
letter in question hardly does any "preaching", certainly not about religion)

As for your demand that people stick to structural biology, may I suggest that 
your reaction to exactly one entry in ccp4bb that elicited almost zero follow 
up (until your comment) feels a bit overblown?  If you strongly disagree with 
Dr Ripple and his colleagues, that is fine, but why shouldn't people at ccp4bb 
occasionally share somewhat orthogonal information?  None of us want to see 
inappropriate content, I am just not sure why you feel that this specific post 
is something that needs to be purged.

Just to be clear - your post does create an impression that you might hold the 
opinion that, as they say, "global warming is a hoax".  Please, let's not have 
further discussion online on the specifics, but I think it might be helpful if 
you could confirm or deny this.

Cheers,

Ed.

---
"I disapprove of what you say, but I will defend to the death your right to say 
it"
Evelyn Beatrice Hall, "The Friends of Voltaire"

On Tue, Aug 20, 2019 at 9:23 PM Daniel M. Himmel, Ph. D. 
mailto:danielmhim...@gmail.com>> wrote:
Dear colleagues,

Since when does being a structural biologist make us experts in climatology,
and isn't it a breach of basic ethical practice and professionalism as 
scientists
to sign on as authors to an article for which we have neither contributed
research nor intellectual content of the manuscript?  Are we now going against
the standard to which the editorial policies of leading reputable biological
journals normally hold us as authors?  And doesn't it hurt the credibility
of a serious scientific article, its authors, and the journal in which it 
appears
if biologists with no expertise in earth science/astrophysics appear
without humility as authors to such an article?

Are you not embarrassed to put your name to an article that uses physical
sciences data as a platform for preaching about religion, politics, and economic
theory ("...social and economic justice for all...")?

Does it not upset you when someone unfamiliar with structural biology draws
firm conclusions that heavily depend on the part of a structural model that has 
high
B-factors?  So why are you unconcerned that you may be guilty of an analogous
error when, as structural biologists, you put your name to a controversial 
interpretation
of selected earth science data?  See, for example,
https://blogs.agu.org/geospace/2017/02/24/living-warm-peak-ice-ages/
 about the ways