[ccp4bb] A topical one...Re: [ccp4bb] Publication ethics Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear Mark, And of course this one is topical:- http://publicationethics.org/case/lost-raw-data Best wishes, John Prof John R Helliwell DSc FInstP CPhys FRSC CChem F Soc Biol. Chair School of Chemistry, University of Manchester, Athena Swan Team. http://www.chemistry.manchester.ac.uk/aboutus/athena/index.html On 27 Apr 2012, at 11:40, Mark J van Raaij mjvanra...@cnb.csic.es wrote: have a look at this case, no danger of your coordinates going to anyone but yourself if you do it this way: http://publicationethics.org/case/author-creates-bogus-email-accounts-proposed-reviewers On 26 Apr 2012, at 12:02, Jrh wrote: Dear Colleagues, I have followed this thread with great interest. It reminds me of the Open Commission Meeting of the Biological Macromolecules Commission in Geneva in 2002 at the IUCr Congress. Ie at which it was concluded that protein coordinates and diffraction data would not be provided to referees. The ethics and rights of readers, authors and referees is a balancing act, as Jeremy and others have emphasised these different constituency's views. The aim of this email though is to draw your attention to the Committee on Publication Ethics (COPE) work and case studies, which are extensive. Ie see:- http://publicationethics.org/ The COPE Forum will also provide advice on case submissions that are made of alleged publication malpractice, various of which are quite subtle. The processes as well though following on from obvious malpractice eg how a university research malpractice committee can be convened are also detailed. Greetings, John Prof John R Helliwell DSc On 26 Apr 2012, at 06:10, Jeremy Tame jt...@tsurumi.yokohama-cu.ac.jp wrote: The problem is it is not the PI who is jumping, it may be a postdoc he/she is throwing. Priority makes careers (look back at the Lavoisier/Priestly, Adams/LeVerrier or Cope/Marsh controversies), and the history of scientific reviewing is not all edifying. Too many checks, not enough balances. Science is probably better served if the author can publish without passing on the pdb model to a potentially unscrupulous reviewer, and if there are minor errors in the published paper then a competing group also has reason to publish its own view. The errors already have to evade the excellent validation tools we now have thanks to so many talented programmers, and proper figures and tables (plus validation report) should be enough for a review. The picture we have of haemoglobin is now much more accurate than the ones which came out decades ago, but those structures were very useful in the mean time. A requirement of resolution better than 2 Angstroms would probably stop poor models entering PDB, but I don't think it would serve science as a whole. Science is generally a self-correcting process, rather than a demand for perfection in every paper. Computer software follows a similar pattern - bug reports don't always invalidate the program. I have happily released data and coordinates via PDB before publication, even back in the 1990s when this was unfashionable, but would not do so if I felt it risked a postdoc failing to publish a key paper before competitors. It might be helpful if journals were more amenable to new structures of solved proteins as the biology often emerges from several models of different conformations or ligation states. But in a publish or perish world, authors need rights too. Reviewers do a necessary job, but there is a need for balance. The attached figure shows a French view of Le Verrier discovering Uranus, while Adams uses his telescope for a quite different purpose. Adams_Leverrier.jpg On Apr 26, 2012, at 2:01 AM, Ethan Merritt wrote: On Wednesday, April 25, 2012 09:40:01 am James Holton wrote: If you want to make a big splash, then don't complain about being asked to leap from a great height. This gets my vote as the best science-related quote of the year. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Publication ethics Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
have a look at this case, no danger of your coordinates going to anyone but yourself if you do it this way: http://publicationethics.org/case/author-creates-bogus-email-accounts-proposed-reviewers On 26 Apr 2012, at 12:02, Jrh wrote: Dear Colleagues, I have followed this thread with great interest. It reminds me of the Open Commission Meeting of the Biological Macromolecules Commission in Geneva in 2002 at the IUCr Congress. Ie at which it was concluded that protein coordinates and diffraction data would not be provided to referees. The ethics and rights of readers, authors and referees is a balancing act, as Jeremy and others have emphasised these different constituency's views. The aim of this email though is to draw your attention to the Committee on Publication Ethics (COPE) work and case studies, which are extensive. Ie see:- http://publicationethics.org/ The COPE Forum will also provide advice on case submissions that are made of alleged publication malpractice, various of which are quite subtle. The processes as well though following on from obvious malpractice eg how a university research malpractice committee can be convened are also detailed. Greetings, John Prof John R Helliwell DSc On 26 Apr 2012, at 06:10, Jeremy Tame jt...@tsurumi.yokohama-cu.ac.jp wrote: The problem is it is not the PI who is jumping, it may be a postdoc he/she is throwing. Priority makes careers (look back at the Lavoisier/Priestly, Adams/LeVerrier or Cope/Marsh controversies), and the history of scientific reviewing is not all edifying. Too many checks, not enough balances. Science is probably better served if the author can publish without passing on the pdb model to a potentially unscrupulous reviewer, and if there are minor errors in the published paper then a competing group also has reason to publish its own view. The errors already have to evade the excellent validation tools we now have thanks to so many talented programmers, and proper figures and tables (plus validation report) should be enough for a review. The picture we have of haemoglobin is now much more accurate than the ones which came out decades ago, but those structures were very useful in the mean time. A requirement of resolution better than 2 Angstroms would probably stop poor models entering PDB, but I don't think it would serve science as a whole. Science is generally a self-correcting process, rather than a demand for perfection in every paper. Computer software follows a similar pattern - bug reports don't always invalidate the program. I have happily released data and coordinates via PDB before publication, even back in the 1990s when this was unfashionable, but would not do so if I felt it risked a postdoc failing to publish a key paper before competitors. It might be helpful if journals were more amenable to new structures of solved proteins as the biology often emerges from several models of different conformations or ligation states. But in a publish or perish world, authors need rights too. Reviewers do a necessary job, but there is a need for balance. The attached figure shows a French view of Le Verrier discovering Uranus, while Adams uses his telescope for a quite different purpose. Adams_Leverrier.jpg On Apr 26, 2012, at 2:01 AM, Ethan Merritt wrote: On Wednesday, April 25, 2012 09:40:01 am James Holton wrote: If you want to make a big splash, then don't complain about being asked to leap from a great height. This gets my vote as the best science-related quote of the year. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] Publication ethics Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear Colleagues, I have followed this thread with great interest. It reminds me of the Open Commission Meeting of the Biological Macromolecules Commission in Geneva in 2002 at the IUCr Congress. Ie at which it was concluded that protein coordinates and diffraction data would not be provided to referees. The ethics and rights of readers, authors and referees is a balancing act, as Jeremy and others have emphasised these different constituency's views. The aim of this email though is to draw your attention to the Committee on Publication Ethics (COPE) work and case studies, which are extensive. Ie see:- http://publicationethics.org/ The COPE Forum will also provide advice on case submissions that are made of alleged publication malpractice, various of which are quite subtle. The processes as well though following on from obvious malpractice eg how a university research malpractice committee can be convened are also detailed. Greetings, John Prof John R Helliwell DSc On 26 Apr 2012, at 06:10, Jeremy Tame jt...@tsurumi.yokohama-cu.ac.jp wrote: The problem is it is not the PI who is jumping, it may be a postdoc he/she is throwing. Priority makes careers (look back at the Lavoisier/Priestly, Adams/LeVerrier or Cope/Marsh controversies), and the history of scientific reviewing is not all edifying. Too many checks, not enough balances. Science is probably better served if the author can publish without passing on the pdb model to a potentially unscrupulous reviewer, and if there are minor errors in the published paper then a competing group also has reason to publish its own view. The errors already have to evade the excellent validation tools we now have thanks to so many talented programmers, and proper figures and tables (plus validation report) should be enough for a review. The picture we have of haemoglobin is now much more accurate than the ones which came out decades ago, but those structures were very useful in the mean time. A requirement of resolution better than 2 Angstroms would probably stop poor models entering PDB, but I don't think it would serve science as a whole. Science is generally a self-correcting process, rather than a demand for perfection in every paper. Computer software follows a similar pattern - bug reports don't always invalidate the program. I have happily released data and coordinates via PDB before publication, even back in the 1990s when this was unfashionable, but would not do so if I felt it risked a postdoc failing to publish a key paper before competitors. It might be helpful if journals were more amenable to new structures of solved proteins as the biology often emerges from several models of different conformations or ligation states. But in a publish or perish world, authors need rights too. Reviewers do a necessary job, but there is a need for balance. The attached figure shows a French view of Le Verrier discovering Uranus, while Adams uses his telescope for a quite different purpose. Adams_Leverrier.jpg On Apr 26, 2012, at 2:01 AM, Ethan Merritt wrote: On Wednesday, April 25, 2012 09:40:01 am James Holton wrote: If you want to make a big splash, then don't complain about being asked to leap from a great height. This gets my vote as the best science-related quote of the year. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear Jeremy, Thank you for the attached cartoon, most warmly welcome by all those in need of a displacement activity in this gruesomely cold and rainy month of April. Oh those terrible French! I know them, I am one of them ;-) . I found the Wikipedia entry on the subject quite entertaining: see http://en.wikipedia.org/wiki/Discovery_of_Neptune The conclusions in the Later analysis section will arouse suspicions that it may have been written by a French author - however the graph given in the previous (Aftermath) section may be of interest, and speak for itself, in our current likelihood-aware and (rightly) validation-obsessed frame of mind. Back to serious things after this culpable diversion ... . With best wishes, Gerard. -- On Thu, Apr 26, 2012 at 02:10:56PM +0900, Jeremy Tame wrote: The problem is it is not the PI who is jumping, it may be a postdoc he/she is throwing. Priority makes careers (look back at the Lavoisier/Priestly, Adams/LeVerrier or Cope/Marsh controversies), and the history of scientific reviewing is not all edifying. Too many checks, not enough balances. Science is probably better served if the author can publish without passing on the pdb model to a potentially unscrupulous reviewer, and if there are minor errors in the published paper then a competing group also has reason to publish its own view. The errors already have to evade the excellent validation tools we now have thanks to so many talented programmers, and proper figures and tables (plus validation report) should be enough for a review. The picture we have of haemoglobin is now much more accurate than the ones which came out decades ago, but those structures were very useful in the mean time. A requirement of resolution better than 2 Angstroms would probably stop poor models entering PDB, but I don't think it would serve science as a whole. Science is generally a self-correcting process, rather than a demand for perfection in every paper. Computer software follows a similar pattern - bug reports don't always invalidate the program. I have happily released data and coordinates via PDB before publication, even back in the 1990s when this was unfashionable, but would not do so if I felt it risked a postdoc failing to publish a key paper before competitors. It might be helpful if journals were more amenable to new structures of solved proteins as the biology often emerges from several models of different conformations or ligation states. But in a publish or perish world, authors need rights too. Reviewers do a necessary job, but there is a need for balance. The attached figure shows a French view of Le Verrier discovering Uranus, while Adams uses his telescope for a quite different purpose. -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
An effective tactic that has not been mentioned yet is simply to attach your coordinates and map to a blanket email and send it simultaneously to all of your competitors. The key thing here is all. Send it to EVERYONE who might serve as a reviewer for your structure. This may sound like madness to your paranoid BIO-whatever colleagues, but try to imagine yourself in your evil competitor's shoes. You have crystals, you've got data sets, you might have even gotten as far as solving the structure and writing a draft manuscript. And then plop! Everything you would need to ruthlessly scoop someone who was kind enough to share their results with you falls in your lap. And everyone in the field knows it! How will your manuscript be received now? Whom will you recommend as reviewers? How will your next grant be received if you now rush out a structure that looks a LOT like something everyone knows is not your work? Looking unethical is far more damaging to your career and future funding that actually being unethical. In a way, the above tactic is a form of publication. It is just self-publication without any peer review to a relatively small audience. Still, a scoop is a scoop? The only problem you will have with your peer-reviewed publication is if your journal of choice has some kind of embargo rule because they want to be the first to make the big splash. Personally, I think all the paranoia and distrust in science today is rooted in this desire for notoriety. Sensationalism and science are a dangerous mix. I know, I know. Journals need advertisers to pay for the pages, etc. etc. Sensationalism is unfortunately connected to the money. But, if you want to make a big splash, then don't complain about being asked to leap from a great height. Anonymous peer review exists because of the need to get an honest answer. Non-anonymous peer review is also a good idea. It is called asking a friend to look at your manuscript. Anyone who has tried the latter can attest to how difficult it can be to get comments back in a timely fashion, if at all! Sometimes even offering to make them a co-author doesn't help. Nevertheless, I highly recommend that everyone do a round of non-anonymous peer review before submitting the manuscript for anonymous peer review. There is nothing more irritating to an official reviewer than someone who clearly submitted a rough draft, and couldn't even be bothered to check for complete sentences, spelling errors, having a point etc. Remember, the anonymous reviewers (and the editor) are the ONLY people who will ever have to read every word of your manuscript. Their comments will usually be less harsh if the MS has already been through non-anonymous peer review. Then again, if a reviewer is asking for your coordinates, then perhaps there is something wrong with your figures? In a way, this is like asking an author for a comma-separated list of their raw data points so that you can re-plot them in Excel. The paper really ought to stand on its own, clearly showing the evidence needed to support the conclusions drawn. Or at least that is what I was taught in scientist school. -James Holton MAD Scientist On 4/18/2012 3:34 PM, Marc Kvansakul wrote: Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over… Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
On Wednesday, April 25, 2012 09:40:01 am James Holton wrote: If you want to make a big splash, then don't complain about being asked to leap from a great height. This gets my vote as the best science-related quote of the year. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
I have to agree with Ed here. I would take it even further and suggest that the PDB file(s) and structure factors SHOULD be requested by the reviewer if many (or even some) of the paper's findings and conclusions depend on map interpretation. Likewise, I would refuse to review if the authors would not comply (which has not happened to me thus far). Bert From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ed Pozharski [epozh...@umaryland.edu] Sent: Friday, April 20, 2012 1:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers It seems that this discussion has somehow reached the conclusion that if a reviewer asks for model/data, there absolutely must be an ulterior motive to cheat you out of your high profile publication. On the other hand, it seems like the intent of such reviewer is also misunderstood as if the only reason would be to catch you fabricating data. I dare to suggest that neither is correct and while this discussion seems to have developed along these lines, both only represent a small fraction of real life situations. I routinely request unreleased data/models. I do it to stem the tide of subprime models in the PDB (outright fabrication is very very rare) and it helps me to form judgment on presented model interpretation (which is more difficult/often impossible to do from 2D figures). If an author refuses to provide data, I would refuse to review. Don't mind my name disclosed in exchange for data, secrecy is for totalitarian governments. Cheers, Ed. On Thu, 2012-04-19 at 20:18 -0400, Edward A. Berry wrote: Bosch, Juergen wrote: To pick a bit on George's point with MR citation. Here's how you can read it in the paper from your favourite competitor: A homology model was generated using [fill in any program for ab initio prediction] and subsequently used for molecular replacement with Molrep. The structure was refined to an Rwork of 21% and Rfree of 24 %. Or maybe the structure was solved by MIR, using a lot of heavy atom data that they had been unable to solve until a fortuitous MR result gave phases which located the heavy atoms -- No, No, it was that new improved version of autosol! Anyway, who cares how the heavy atoms were located- the structure was solved entirely using their data and they have the raw data (image files even) to prove it. It was just bad luck with the derivatives that kept them from solving it 6 months earlier. They really deserve to have the first publication! -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
I agree completely with Ed and made a similar suggestion when this
discussion came up last time i.e. the reviewer should reveal the identity
if he wants coordinates. Even data (including raw data if need be) can be
given in those cases. As reviewer has a reason to suspect and therefore
want to inspect the data implicated in the manuscript of the author(s), the
author(s) has every reason to suspect the motive of such reviewers
('Reviewers' are not 'gods' or a different breed, they are future 'authors'
of papers and proposals).
While almost always we find that 'reviewers' dont indulge in any kind of
malpractices and are very useful in improving the quality of manuscripts,
there are rarest of rare scenarios when one also encounters reviewer
'misconduct'. More so if you do not belong to certain clubs or the high
profile niches/regions of research.
A reviewer(may be a competitor but one who does not come out explicitly
with a conflict of interest) need not use just data only, but can also get
clues/ideas presented in the manuscript to scoop. To narrate a situation
that happened to us several years back, this 'reviewer' played a delaying
tactics by asking for more data to be included in the manuscript (did not
reject though), which were not relevant at all. The editor who handled the
manuscript was a serious one, luckily for us, and accepted our argument
that it was not required. The paper was accepted but it had to wait for
publication in the journal. Before it was published, we saw a paper
appearing in another journal (submitted after acceptance of our paper) and
accepted for publication in a few days with Immediate Online Publication.
The paper had the claims, very similar to ones made in our paper, from a
half baked story on a structure of a homologous system. The corresponding
author of the paper was the first reviewer (as we thought he/she was an
authority in the area!!!) whom we suggested. When we contacted the editor
to reveal the identity of the 'reviewer' by mentioning the case, a mute
reply(apology!) came that they are sorry that this has happened. Also, I
must add that these situations are more likely when the claims are high
(read as higher journal impact factor!).
The above scenario, if it happens when one is reasonably established, would
not affect the individual as much as it would have affected someone in the
beginning of his/her career. I am tempted to favour, at this point of time
of my career, the suggestion to part not only with the PDB but even with
raw data at the time of submission. However, considering the non ideal
systems that we have to deal with, I would expect the community to put a
rider to stop the rarest of rare 'reviewer' misconducts, even though it
can only be a costly affair to a handful!
-Sankar
On Fri, Apr 20, 2012 at 10:38 PM, Ed Pozharski epozh...@umaryland.eduwrote:
Manoj,
while reviewer-bashing is my favorite pastime too (recent gem: studying
transcription factors will not advance our understanding of mechanistic
enzymology), you should remember that they are unpaid individuals who
volunteer their time to help you to improve your paper (or so the idea
goes). It is also important to recognize that the editor accepts the
paper, not the reviewer (who acts in advisory capacity).
A much better alternative to your draconian list was already mentioned -
I'll give you my data if you tell me who you are. Works for me.
Cheers,
Ed.
On Fri, 2012-04-20 at 11:07 -0400, Manoj Tiwari wrote:
1) The reviewer should be given at most 24-48 hours of time to give
comments after receiving the data.
2) (S)he should declare to the editor that the paper is going to be
accepted if everything with the data/model is okay. The reviewer
should also send comments to author on what does (s)he intend to
examine in the structure.
3) After going through the model/data, the reviewer's comment should
be exclusively based on the structure or its correlation with the
experimental data.
4) If reviewer finds any mistake which can not be corrected or which
changes the theme of the paper and the reviewer rejects the paper, the
responsibility should lie on author. But certainly the editor or a
team decided by editor should ensure that when the paper is rejected
at this stage, the reason for rejection is valid and the mistakes can
not be rectified. Editor should also ensure that authors are given
sufficient opportunity to correct the mistake if possible.
--
I don't know why the sacrifice thing didn't work.
Science behind it seemed so solid.
Julian, King of Lemurs
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
(my last spam) This is very true. Compared to biomedicine, protein crystallographers are holy saints: Of 50 landmark papers in oncology, people from Amgen could only reproduce 6 (11%) and in a similar study, people at Bayer could only reproduce 14 out of 67 (21%) studies. Even more troubling, non-reproducible papers got cited more often then reproducible ones. I really hope the bubble will collapse soon since it led (leads) to the waste of billions of research euros (in industry and academia) and the testing of ineffective compounds on patients. Sorry for this off-topic remark, Herman http://www.nature.com/nature/journal/v483/n7391/full/483531a.html http://www.nature.com/nrd/journal/v10/n9/full/nrd3439-c1.html -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Miguel Ortiz Lombardia Sent: Thursday, April 19, 2012 9:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers El 19/04/12 18:42, Patrick Loll escribió: Well, it is clear from this comment that in different fields there are different rules... . In macromolecular Xtallolgraphy, where some people deal with biologists from biomedical sciences, the impact of journals is an important aspect during evaluation and, unfortunately, pre-publication review of structures has no actual value in their field. For a structural BIO-logist in biomedical sciences, a paper it is not just a paper, it is an effort of years reduced to a (or few) paper(s). The non-structural BIO-people understand what is a Cell paper, but not at all about what it is a pre-publication of a structure. My thougts go in the direction of grant applications, fellowships, promotion, all filtered by the impact factor but not by pre-publication of structures which, btw, it is neither considered in the h-index of a researcher. Oh what the hell, someone else poured the gasoline, I may as well supply a lit match: What Maria says is absolutely true--I dwell among biologists, so I fully understand the rules of the field. But it's not so clear that these rules are good ones. Biology is obsessed with high impact, and I argue science is ill served by this preoccupation. The highest impact-factor journals seem to have the highest number of retractions (see this past Tuesday's New York Times Science section for a discussion). And in this forum it's certainly germane to note that the technical quality of published structures is, on average, poorer in the highest impact journals (at least by some criteria; see the paper from Brown Ramaswamy in Acta Crystallogr D63: 941-50 (2007)). Pat -- - Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu Indeed the rules are clearly bad. They're actually a mirror of the rules of political economy in our western/capitalist/call-them-as-you-want societies. Actually, expect bubble collapses in the biological field. Perhaps not spectacular, most probably not everything-falling-at-once, but surely not without serious implications. We also have our too-big-to-fall paradigms, especially in bio-medicine. In any case, the rules are there and for most of the people who intend to keep working (most often working as in job, not as in art) in biological science (with or without double quotes) it is certainly easier to bow to them than to resist them. Understandably, for the latter option is most often punished sooner or later, with no shame, by those who exclude you from the so-called excellence club. It would help if some big, truly respected names in biology would attack seriously these rules and put clear the damage they are causing to biological science. Some do, I'm now thinking of Peter Lawrence for example, but they are too few to be anything else than 'lone rangers'. It would be certainly even more helpful if we could unite and collectively reject this state of affairs. But this is, for several reasons that would need a far too-long text for a bulletin board post, less expected than rain on the desert. Whatever the case, we bio-crystallographers are a very small set of the people working in biology. We may now and then have this kind of discussion where we put forward our concerns, our idealistic view of the peer review system, etc. Move aside, go to a lab of almost any other field in biology and tell them about these discussions; most of the time they will look at you as they would at a Martian. Back to the original post: I have never been requested coordinates/data. It's however clear to me that if the reviewer wants to see them (s)he has the right to do so. The problem
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
When I hear of a reviewer holding up a publication and then publishing something similar, my first reaction is fury and I feel the case should be investigated and this immoral individual should be exposed. However I can see that there are many shades of gray here. We're all biased in that we tend to ignore information that conflicts with our previous cherished beliefs and focus on things that confirm them. So it can take a long time to change your mind - sometimes months. This can lead to indecision and delays, but in retrospect we tend to think that we would have come to those conclusions in any case so there's no harm in using the info. People with a strong sense of duty will get the review done quickly and make sure that they don't take advantage of the data, but I can see that it can be tempting. I think the idea of getting reviewers to sign a piece of paper saying that there is no immediate conflict of interest i.e. they are not about to publish something similar, is a good one. The author could prepare simple statement describing the topics covered (not the abstract which gives, or should give, the conclusions). Then it's not a matter of proving that the reviewer cheated, only that they had the opportunity to cheat. I always communicate freely with the editors, e.g. telling them why I don't want such-and-such to review the paper. Wouldn't it be possible simply to ask the editor to check that the reviewer asking for co-ordinates etc is not close to publishing something that could benefit from the data? I don't think it's a good idea for reviewers' names to be visible because that would mean that we would all have to do a far more professional job of the review. (I'm not a career scientist but I've been asked to review a few papers.) I also agree with those who say that this competitive focus on high impact journals etc. stifles creativity, is inefficient and gives poor value for money. Just some thoughts - probably stating the obvious Patrick On 20 April 2012 01:18, Edward A. Berry ber...@upstate.edu wrote: Bosch, Juergen wrote: To pick a bit on George's point with MR citation. Here's how you can read it in the paper from your favourite competitor: A homology model was generated using [fill in any program for ab initio prediction] and subsequently used for molecular replacement with Molrep. The structure was refined to an Rwork of 21% and Rfree of 24 %. Or maybe the structure was solved by MIR, using a lot of heavy atom data that they had been unable to solve until a fortuitous MR result gave phases which located the heavy atoms -- No, No, it was that new improved version of autosol! Anyway, who cares how the heavy atoms were located- the structure was solved entirely using their data and they have the raw data (image files even) to prove it. It was just bad luck with the derivatives that kept them from solving it 6 months earlier. They really deserve to have the first publication! -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Just a thought: When a reviewer asks for the model/data, 1) The reviewer should be given at most 24-48 hours of time to give comments after receiving the data. 2) (S)he should declare to the editor that the paper is going to be accepted if everything with the data/model is okay. The reviewer should also send comments to author on what does (s)he intend to examine in the structure. 3) After going through the model/data, the reviewer's comment should be exclusively based on the structure or its correlation with the experimental data. 4) If reviewer finds any mistake which can not be corrected or which changes the theme of the paper and the reviewer rejects the paper, the responsibility should lie on author. But certainly the editor or a team decided by editor should ensure that when the paper is rejected at this stage, the reason for rejection is valid and the mistakes can not be rectified. Editor should also ensure that authors are given sufficient opportunity to correct the mistake if possible. Thanks MT On Fri, Apr 20, 2012 at 6:23 AM, Patrick Shaw Stewart patr...@douglas.co.uk wrote: When I hear of a reviewer holding up a publication and then publishing something similar, my first reaction is fury and I feel the case should be investigated and this immoral individual should be exposed. However I can see that there are many shades of gray here. We're all biased in that we tend to ignore information that conflicts with our previous cherished beliefs and focus on things that confirm them. So it can take a long time to change your mind - sometimes months. This can lead to indecision and delays, but in retrospect we tend to think that we would have come to those conclusions in any case so there's no harm in using the info. People with a strong sense of duty will get the review done quickly and make sure that they don't take advantage of the data, but I can see that it can be tempting. I think the idea of getting reviewers to sign a piece of paper saying that there is no immediate conflict of interest i.e. they are not about to publish something similar, is a good one. The author could prepare simple statement describing the topics covered (not the abstract which gives, or should give, the conclusions). Then it's not a matter of proving that the reviewer cheated, only that they had the opportunity to cheat. I always communicate freely with the editors, e.g. telling them why I don't want such-and-such to review the paper. Wouldn't it be possible simply to ask the editor to check that the reviewer asking for co-ordinates etc is not close to publishing something that could benefit from the data? I don't think it's a good idea for reviewers' names to be visible because that would mean that we would all have to do a far more professional job of the review. (I'm not a career scientist but I've been asked to review a few papers.) I also agree with those who say that this competitive focus on high impact journals etc. stifles creativity, is inefficient and gives poor value for money. Just some thoughts - probably stating the obvious Patrick On 20 April 2012 01:18, Edward A. Berry ber...@upstate.edu wrote: Bosch, Juergen wrote: To pick a bit on George's point with MR citation. Here's how you can read it in the paper from your favourite competitor: A homology model was generated using [fill in any program for ab initio prediction] and subsequently used for molecular replacement with Molrep. The structure was refined to an Rwork of 21% and Rfree of 24 %. Or maybe the structure was solved by MIR, using a lot of heavy atom data that they had been unable to solve until a fortuitous MR result gave phases which located the heavy atoms -- No, No, it was that new improved version of autosol! Anyway, who cares how the heavy atoms were located- the structure was solved entirely using their data and they have the raw data (image files even) to prove it. It was just bad luck with the derivatives that kept them from solving it 6 months earlier. They really deserve to have the first publication! -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
It seems that this discussion has somehow reached the conclusion that if a reviewer asks for model/data, there absolutely must be an ulterior motive to cheat you out of your high profile publication. On the other hand, it seems like the intent of such reviewer is also misunderstood as if the only reason would be to catch you fabricating data. I dare to suggest that neither is correct and while this discussion seems to have developed along these lines, both only represent a small fraction of real life situations. I routinely request unreleased data/models. I do it to stem the tide of subprime models in the PDB (outright fabrication is very very rare) and it helps me to form judgment on presented model interpretation (which is more difficult/often impossible to do from 2D figures). If an author refuses to provide data, I would refuse to review. Don't mind my name disclosed in exchange for data, secrecy is for totalitarian governments. Cheers, Ed. On Thu, 2012-04-19 at 20:18 -0400, Edward A. Berry wrote: Bosch, Juergen wrote: To pick a bit on George's point with MR citation. Here's how you can read it in the paper from your favourite competitor: A homology model was generated using [fill in any program for ab initio prediction] and subsequently used for molecular replacement with Molrep. The structure was refined to an Rwork of 21% and Rfree of 24 %. Or maybe the structure was solved by MIR, using a lot of heavy atom data that they had been unable to solve until a fortuitous MR result gave phases which located the heavy atoms -- No, No, it was that new improved version of autosol! Anyway, who cares how the heavy atoms were located- the structure was solved entirely using their data and they have the raw data (image files even) to prove it. It was just bad luck with the derivatives that kept them from solving it 6 months earlier. They really deserve to have the first publication! -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear Marc, The only way a reviewer can really judge the quality ofa structure and verify the claims made in a structural biology manuscript is by having access to the pdb files and x-ray data. I have myself as a reviewer requested co-ordinates and data for this purpose, and the results can be quite revealing, both in positive and negative sense. I have no problem myself to provide data when requested and even to release structures before publication. The latter has helped me for a paper that was accepted last week where one of the referees wrote in hes/her report that he/she could only judge the paper correctly because the data were available for downloading. Thus I am a strong advocate for all structural data to be made available to referees upon submission of a manuscript. Science and scientific publishing requires a great deal of mutual trust. This is not only for the reader or referee who has to trust that the work is correct and not fraudulent. It also goes in the opposite way where the author has to trust the referees and editors to be honest. Only in this way can the system work. Otherwise, just keep everything for yourself and don't publish. In the 23 years that I am active in science I had only a single case where I genuinely believe a referee misused his position. This to say that 99.99% of the referee reports are honest, although not necessarily in agreement with your own vision. Remy Loris Vrije Universiteit Brussel and VIB On 19/04/12 00:34, Marc Kvansakul wrote: Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over… Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear Marc, As a reviewer I find it difficult to “visualise” a structure based on a static 2D figure. I echo Joel's comments. If the (unreleased) coordinates are not supplied by the authors on request, I would simply refuse to review the paper on that ground. I suppose one can trust a reputable journal on the confidentiality issue. Wai -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Hi, Just to add on Joel's remarks: I had a case where I reviewed a paper for which the coordinates and SF's have already been released. By looking at the e.d. map (from the EDS server) I could spot a mistake in the tracing of one important spot (which happened to be near the active site - no I didn't go through the whole map!)- a peptide had to be flipped. I pointed this out to the authors and it was corrected (I assume, I never went back to check). The more common situation of course is that of data not being released until after publication. I suspect that after the discussions we've been through recently, unwillingness to provide data to Editor/Reviewer may well raise questions. Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Joel Tyndall [joel.tynd...@otago.ac.nz] Sent: Thursday, April 19, 2012 7:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers Marc, As someone with limited experience in publishing structures but with other experience reviewing the same I feel strongly about this. I am hoping to submit any future papers with the pdb structure already released or submit the coordinates as supplementary material. As a reviewer I find it difficult to “visualise” a structure based on a static 2D figure. I would like to see coordinates/structure factors supplied for review or released on the pdb. I believe that if released on the pdb then this should give you enough security that it is still your structure. Just my thoughts Joel From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marc Kvansakul Sent: Thursday, 19 April 2012 10:34 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Off-topic: Supplying PDB file to reviewers Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over… Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Hi, There is the exact same problem when releasing a software, possibly open source, before the corresponding article is accepted. And I don't know a correct solution to this problem. Regards, F. On 04/19/2012 05:34 PM, Yu Wai Chen wrote: Dear Marc, As a reviewer I find it difficult to “visualise” a structure based on a static 2D figure. I echo Joel's comments. If the (unreleased) coordinates are not supplied by the authors on request, I would simply refuse to review the paper on that ground. I suppose one can trust a reputable journal on the confidentiality issue. Wai -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Thanks a lot to everyone for their insightful comments I certainly had an interesting day trying to digest all that was said! Although my initial reaction to the request was to turn it down since I had never heard of such a request before, I decided in the end to accede to the request, since not doing so would imply that all reviewers are simply out there to get me. To quote one email that I received Being paranoid is good, but you can't let it interfere with publishingŠ. Whilst on occasion this may be true, I would certainly hope it is not the norm. Without going into detail here there are some unusual topological aspects about the structure that could justify requesting the coordinates, so hopefully whoever is receiving the file will just sit back and enjoy the structure as much as I did, and produce a better review in the end that could not have been produced without the access. Best wishes Marc On 19/04/12 7:25 PM, Francois Berenger beren...@riken.jp wrote: Hi, There is the exact same problem when releasing a software, possibly open source, before the corresponding article is accepted. And I don't know a correct solution to this problem. Regards, F. On 04/19/2012 05:34 PM, Yu Wai Chen wrote: Dear Marc, As a reviewer I find it difficult to ³visualise² a structure based on a static 2D figure. I echo Joel's comments. If the (unreleased) coordinates are not supplied by the authors on request, I would simply refuse to review the paper on that ground. I suppose one can trust a reputable journal on the confidentiality issue. Wai -- Yu Wai Chen, PhDLecturer King's College London, Randall Division +44-207-848-8206 New Hunt's House, Guy's Campus, London SE1 1UL, U.K.
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone else's results gets away without any risk of being caught. Besides making the name of the reviewer public, I see other options: 1) submit the coordinates and structure factors to the pdb to get a priority date as has been suggested before. Many journals require anyways a pdb code before acceptance of the paper. One could even publish this priority date in the paper in the footnote where the pdb code is mentioned. 2) require from referees a conflict-of-interest-statement that they, or close colleagues are not working on the same or a very similar structure. If an author gets the impression that he may have been scooped by a less-ethical referee, he could ask the journal to verify that the referees of his rejected paper were not involved in the accelerated publication. If it turns out that a referee has made a false statement this would clearly constitute fraud and a reason for repercussions. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jobichen Chacko Sent: Thursday, April 19, 2012 2:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers Dear All, Here comes the problem of blind reveiw, the authors are always at the receving end to share all there data, results and now the full cordinates to an unknown person, just trusting the journal editor. Why don't the journals think about making the name of the reviewer also public. Eventhough the persons advocated giving the cordinates, there were cases of holding the paper for reveiw for few months and finally rejecting it, while a very close article appeared as accelerated publn within few weeks of rejection of the original paper. Refer to the previous discussion on fake structure. Again it depends on how close you are towards the acceptance. Also hesitation to give away your cordiantes without any guarantee of publishing it in that journal cannot be considered as a big sin, especially if someone's graduation is depend on a single paper. Jobi On Thu, Apr 19, 2012 at 6:34 AM, Marc Kvansakul m.kvansa...@latrobe.edu.au wrote: Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over... Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Colin, Speaking as someone who has one foot in small molecule crystallography and the other in macromolecular, I have to say that attitudes are completely different, and that there are good reasons for this. A PhD student or junior postdoc in a macromolecular lab may have spent the last three (or more) years cloning, expressing. purifying and crystallizing a protein, and it is very likely that three or more groups elsewhere in the world are working on the same target. Even if the organisms are different, usually only one group will be able to publish in a high-profile journal, so being scooped is a major worry and happens frequently, even when all concerned are completely honest. A single small molecule structure is a very much smaller part of the average chemical PhD which often involves dozens of structures, and a couple of duplicated structures will have little influence on the future career of the PhD student. Releasing the PDB hold on a structure just before submitting the paper has something to be said for it. I would like to do this more often, but it is usually vetoed by paranoid biological co-authors. Even if one is providing the competition with a good MR model, at least they will have to cite it. George On 04/19/2012 03:09 PM, Colin Groom wrote: It has always struck me as something of a surprise that pre-publication review of structures in protein-land differs so significantly from small molecule-land. One of the activities of the CCDC is to supply pre-release CSD structures to referees, using a simple, automated system to establish that the requestors are referees. This avoids the need for any involvement of the depositor or journal and allows a centralised record to be kept as to who saw which structures and when (although, to my knowledge, we have never needed to refer to this). In 2012, requests have averaged at about 5 a day, but the real figure is probably much higher, as some journals provide this facility themselves. The sense I get from the small-molecule community is that they (we) have a great degree of well placed trust and see real value in pre-publication review of structures, not just papers - I'm sure this is true for the overwhelming majority of the macromolecular world too. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: 19 April 2012 13:54 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone else's results gets away without any risk of being caught. Besides making the name of the reviewer public, I see other options: 1) submit the coordinates and structure factors to the pdb to get a priority date as has been suggested before. Many journals require anyways a pdb code before acceptance of the paper. One could even publish this priority date in the paper in the footnote where the pdb code is mentioned. 2) require from referees a conflict-of-interest-statement that they, or close colleagues are not working on the same or a very similar structure. If an author gets the impression that he may have been scooped by a less-ethical referee, he could ask the journal to verify that the referees of his rejected paper were not involved in the accelerated publication. If it turns out that a referee has made a false statement this would clearly constitute fraud and a reason for repercussions. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jobichen Chacko Sent: Thursday, April 19, 2012 2:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers Dear All, Here comes the problem of blind reveiw, the authors are always at the receving end to share all there data, results and now the full cordinates to an unknown person, just trusting the journal editor. Why don't the journals think about making the name of the reviewer also public. Eventhough the persons advocated giving the cordinates, there were cases of holding the paper for reveiw for few months and finally rejecting it, while a very close article appeared as accelerated publn within few weeks of rejection of the original paper. Refer to the previous discussion on fake structure. Again it depends on how close you are towards the acceptance. Also hesitation to give away your cordiantes without any guarantee of publishing it in that journal cannot be considered as a big sin, especially if someone's graduation is depend on a single paper. Jobi On Thu, Apr 19, 2012 at 6:34 AM, Marc Kvansakul m.kvansa...@latrobe.edu.au wrote: Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
This subject raised (and keeps raising) its head above the parapet not all that long ago on this bulletin board. Maybe it's time to bite the bullet and try and do something about it? I would like to see and can imagine the following scenario... something I have tentatively suggested before... There is a secure web server (at the PDB?) where you can upload your coordinates and structure factor file - a Pre-release server if you will. On uploading you are then given a unique URL which can be provided to a journal and passed on to any selected reviewer. Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. This way reviewers can see the model, and the density that the authors have built into, but not have any access to either the coordinate file or mtz - and sti make an informed judgment. With regards, from a tilting pendolino train, somewhere in the bowels of south -east England. Tony. On 19 Apr 2012, at 14:55, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Colin, Speaking as someone who has one foot in small molecule crystallography and the other in macromolecular, I have to say that attitudes are completely different, and that there are good reasons for this. A PhD student or junior postdoc in a macromolecular lab may have spent the last three (or more) years cloning, expressing. purifying and crystallizing a protein, and it is very likely that three or more groups elsewhere in the world are working on the same target. Even if the organisms are different, usually only one group will be able to publish in a high-profile journal, so being scooped is a major worry and happens frequently, even when all concerned are completely honest. A single small molecule structure is a very much smaller part of the average chemical PhD which often involves dozens of structures, and a couple of duplicated structures will have little influence on the future career of the PhD student. Releasing the PDB hold on a structure just before submitting the paper has something to be said for it. I would like to do this more often, but it is usually vetoed by paranoid biological co-authors. Even if one is providing the competition with a good MR model, at least they will have to cite it. George On 04/19/2012 03:09 PM, Colin Groom wrote: It has always struck me as something of a surprise that pre-publication review of structures in protein-land differs so significantly from small molecule-land. One of the activities of the CCDC is to supply pre-release CSD structures to referees, using a simple, automated system to establish that the requestors are referees. This avoids the need for any involvement of the depositor or journal and allows a centralised record to be kept as to who saw which structures and when (although, to my knowledge, we have never needed to refer to this). In 2012, requests have averaged at about 5 a day, but the real figure is probably much higher, as some journals provide this facility themselves. The sense I get from the small-molecule community is that they (we) have a great degree of well placed trust and see real value in pre-publication review of structures, not just papers - I'm sure this is true for the overwhelming majority of the macromolecular world too. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: 19 April 2012 13:54 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone else's results gets away without any risk of being caught. Besides making the name of the reviewer public, I see other options: 1) submit the coordinates and structure factors to the pdb to get a priority date as has been suggested before. Many journals require anyways a pdb code before acceptance of the paper. One could even publish this priority date in the paper in the footnote where the pdb code is mentioned. 2) require from referees a conflict-of-interest-statement that they, or close colleagues are not working on the same or a very similar structure. If an author gets the impression that he may have been scooped by a less-ethical referee, he could ask the journal to verify that the referees of his rejected paper were not involved in the accelerated publication. If it turns out that a referee has made a false statement this would clearly constitute fraud and a reason for repercussions. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jobichen Chacko Sent: Thursday, April 19, 2012 2:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
The idea of referees being given a link to the structure at the PDB came up in discussions with PDB people, when we were preparing our X-ray validation report. Among other potential issues, it would be a lot of work for them to set up a secure password-protected system, and the growth in the PDB keeps them pretty busy doing other things. The upcoming validation report is meant to satisfy most of what referees would want to know about the structure and its fit to the data. If it raises some flags, then they have a good excuse to ask for more, through the journal. On the suggestion of a pre-release server: if you allow someone to rotate a molecule and take several screenshots of it from different orientations, you might as well give them the coordinates because that's all you need to reconstruct them pretty precisely. For those who know how to compile Fortran programs, Michael Rossmann wrote a program years ago that will extract coordinates from a stereo pair, and I'm sure one could do much better with multiple images. Regards, Randy Read On 19 Apr 2012, at 15:09, Antony Oliver wrote: This subject raised (and keeps raising) its head above the parapet not all that long ago on this bulletin board. Maybe it's time to bite the bullet and try and do something about it? I would like to see and can imagine the following scenario... something I have tentatively suggested before... There is a secure web server (at the PDB?) where you can upload your coordinates and structure factor file - a Pre-release server if you will. On uploading you are then given a unique URL which can be provided to a journal and passed on to any selected reviewer. Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. This way reviewers can see the model, and the density that the authors have built into, but not have any access to either the coordinate file or mtz - and sti make an informed judgment. With regards, from a tilting pendolino train, somewhere in the bowels of south -east England. Tony. On 19 Apr 2012, at 14:55, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: Colin, Speaking as someone who has one foot in small molecule crystallography and the other in macromolecular, I have to say that attitudes are completely different, and that there are good reasons for this. A PhD student or junior postdoc in a macromolecular lab may have spent the last three (or more) years cloning, expressing. purifying and crystallizing a protein, and it is very likely that three or more groups elsewhere in the world are working on the same target. Even if the organisms are different, usually only one group will be able to publish in a high-profile journal, so being scooped is a major worry and happens frequently, even when all concerned are completely honest. A single small molecule structure is a very much smaller part of the average chemical PhD which often involves dozens of structures, and a couple of duplicated structures will have little influence on the future career of the PhD student. Releasing the PDB hold on a structure just before submitting the paper has something to be said for it. I would like to do this more often, but it is usually vetoed by paranoid biological co-authors. Even if one is providing the competition with a good MR model, at least they will have to cite it. George On 04/19/2012 03:09 PM, Colin Groom wrote: It has always struck me as something of a surprise that pre-publication review of structures in protein-land differs so significantly from small molecule-land. One of the activities of the CCDC is to supply pre-release CSD structures to referees, using a simple, automated system to establish that the requestors are referees. This avoids the need for any involvement of the depositor or journal and allows a centralised record to be kept as to who saw which structures and when (although, to my knowledge, we have never needed to refer to this). In 2012, requests have averaged at about 5 a day, but the real figure is probably much higher, as some journals provide this facility themselves. The sense I get from the small-molecule community is that they (we) have a great degree of well placed trust and see real value in pre-publication review of structures, not just papers - I'm sure this is true for the overwhelming majority of the macromolecular world too. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: 19 April 2012 13:54 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. Anthony, it would have to be something other than AstexViewer since the distributed version at least allows you to do a Save As on the co-ordinates (not the maps though, but I guess the co-ordinates are the main point at issue). In any case I agree with Randy that there are problems with this. Cheers -- Ian
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
and allows a centralised record to be kept as to who saw which structures and when (although, to my knowledge, we have never needed to refer to this). In 2012, requests have averaged at about 5 a day, but the real figure is probably much higher, as some journals provide this facility themselves. The sense I get from the small-molecule community is that they (we) have a great degree of well placed trust and see real value in pre-publication review of structures, not just papers - I'm sure this is true for the overwhelming majority of the macromolecular world too. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: 19 April 2012 13:54 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone else's results gets away without any risk of being caught. Besides making the name of the reviewer public, I see other options: 1) submit the coordinates and structure factors to the pdb to get a priority date as has been suggested before. Many journals require anyways a pdb code before acceptance of the paper. One could even publish this priority date in the paper in the footnote where the pdb code is mentioned. 2) require from referees a conflict-of-interest-statement that they, or close colleagues are not working on the same or a very similar structure. If an author gets the impression that he may have been scooped by a less-ethical referee, he could ask the journal to verify that the referees of his rejected paper were not involved in the accelerated publication. If it turns out that a referee has made a false statement this would clearly constitute fraud and a reason for repercussions. Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jobichen Chacko Sent: Thursday, April 19, 2012 2:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers Dear All, Here comes the problem of blind reveiw, the authors are always at the receving end to share all there data, results and now the full cordinates to an unknown person, just trusting the journal editor. Why don't the journals think about making the name of the reviewer also public. Eventhough the persons advocated giving the cordinates, there were cases of holding the paper for reveiw for few months and finally rejecting it, while a very close article appeared as accelerated publn within few weeks of rejection of the original paper. Refer to the previous discussion on fake structure. Again it depends on how close you are towards the acceptance. Also hesitation to give away your cordiantes without any guarantee of publishing it in that journal cannot be considered as a big sin, especially if someone's graduation is depend on a single paper. Jobi On Thu, Apr 19, 2012 at 6:34 AM, Marc Kvansakul m.kvansa...@latrobe.edu.au wrote: Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over... Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au | LEGAL NOTICE Unless expressly stated otherwise, information contained in this message is confidential. If this message is not intended for you, please inform postmas...@ccdc.cam.ac.uk and delete the message. The Cambridge Crystallographic Data Centre is a company Limited by Guarantee and a Registered Charity. Registered in England No. 2155347 Registered Charity No. 800579 Registered office 12 Union Road, Cambridge CB2 1EZ. -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Thanks Ian, Of course it'd have to be something else :-) but the capability of displaying models and maps via a web-browser is at least within current capabilities. Perhaps the whole model or electron density doesn't need to be presented - perhaps just a representative chunk or chunks with the best and worst bits of the model and maps (highest / lowest B-factors, Density/Model correlation ? ) thereby preventing theft by Fortran Script...? This is all, of course, just a bit of a thought experiment - and there are bound to be problems and issues with such a system - but I think it *is* something that could possibly be implemented and would certainly (in my humble opinion) be useful for potential reviewers, myself included. Tony. On 19 Apr 2012, at 15:47, Ian Tickle ianj...@gmail.com wrote: Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. Anthony, it would have to be something other than AstexViewer since the distributed version at least allows you to do a Save As on the co-ordinates (not the maps though, but I guess the co-ordinates are the main point at issue). In any case I agree with Randy that there are problems with this. Cheers -- Ian
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Hi I would just like to note that a web-browser plug in is on the client machine - to view a PDB file in any viewer like this (ie Astex-viewer, jmol) requires that file to be physically downloaded onto the client computer - and put into the TEMP folder of that machine. As such, the act of viewing the coordinate data in a viewer has by definition downloaded the data onto the reviewers computer where they will have complete and unrestricted access if they know where to look. Regards Tom This subject raised (and keeps raising) its head above the parapet not all that long ago on this bulletin board. Maybe it's time to bite the bullet and try and do something about it? I would like to see and can imagine the following scenario... something I have tentatively suggested before... There is a secure web server (at the PDB?) where you can upload your coordinates and structure factor file - a Pre-release server if you will. On uploading you are then given a unique URL which can be provided to a journal and passed on to any selected reviewer. Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. This way reviewers can see the model, and the density that the authors have built into, but not have any access to either the coordinate file or mtz - and sti make an informed judgment. With regards, from a tilting pendolino train, somewhere in the bowels of south -east England. Tony. On 19 Apr 2012, at 14:55, George M. Sheldrickgshe...@shelx.uni-ac.gwdg.de wrote: Colin, Speaking as someone who has one foot in small molecule crystallography and the other in macromolecular, I have to say that attitudes are completely different, and that there are good reasons for this. A PhD student or junior postdoc in a macromolecular lab may have spent the last three (or more) years cloning, expressing. purifying and crystallizing a protein, and it is very likely that three or more groups elsewhere in the world are working on the same target. Even if the organisms are different, usually only one group will be able to publish in a high-profile journal, so being scooped is a major worry and happens frequently, even when all concerned are completely honest. A single small molecule structure is a very much smaller part of the average chemical PhD which often involves dozens of structures, and a couple of duplicated structures will have little influence on the future career of the PhD student. Releasing the PDB hold on a structure just before submitting the paper has something to be said for it. I would like to do this more often, but it is usually vetoed by paranoid biological co-authors. Even if one is providing the competition with a good MR model, at least they will have to cite it. George On 04/19/2012 03:09 PM, Colin Groom wrote: It has always struck me as something of a surprise that pre-publication review of structures in protein-land differs so significantly from small molecule-land. One of the activities of the CCDC is to supply pre-release CSD structures to referees, using a simple, automated system to establish that the requestors are referees. This avoids the need for any involvement of the depositor or journal and allows a centralised record to be kept as to who saw which structures and when (although, to my knowledge, we have never needed to refer to this). In 2012, requests have averaged at about 5 a day, but the real figure is probably much higher, as some journals provide this facility themselves. The sense I get from the small-molecule community is that they (we) have a great degree of well placed trust and see real value in pre-publication review of structures, not just papers - I'm sure this is true for the overwhelming majority of the macromolecular world too. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: 19 April 2012 13:54 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone else's results gets away without any risk of being caught. Besides making the name of the reviewer public, I see other options: 1) submit the coordinates and structure factors to the pdb to get a priority date as has been suggested before. Many journals require anyways a pdb code before acceptance of the paper. One could even publish this priority date in the paper in the footnote where the pdb code is mentioned. 2) require from referees a conflict-of-interest-statement that they, or close colleagues are not working on the same or a very similar structure. If an author gets the impression that he may have been scooped by a less-ethical referee, he could ask the journal to verify that the referees
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Tom, that's indeed true. But, the file can be encrypted, and it doesn't necessarily have to be in strict PDB format. Getting out of my comfort and knowledge zone here... But with the advent of HTML5 is a plugin strictly necessary? Tony. Plus if you're only looking at a chunk of structure - you wouldn't have enough data to be an issue? On 19 Apr 2012, at 16:20, Tom Oldfield oldfi...@ebi.ac.uk wrote: Hi I would just like to note that a web-browser plug in is on the client machine - to view a PDB file in any viewer like this (ie Astex-viewer, jmol) requires that file to be physically downloaded onto the client computer - and put into the TEMP folder of that machine. As such, the act of viewing the coordinate data in a viewer has by definition downloaded the data onto the reviewers computer where they will have complete and unrestricted access if they know where to look. Regards Tom This subject raised (and keeps raising) its head above the parapet not all that long ago on this bulletin board. Maybe it's time to bite the bullet and try and do something about it? I would like to see and can imagine the following scenario... something I have tentatively suggested before... There is a secure web server (at the PDB?) where you can upload your coordinates and structure factor file - a Pre-release server if you will. On uploading you are then given a unique URL which can be provided to a journal and passed on to any selected reviewer. Crucially this does *not* allow the coordinates or maps to be downloaded, but visually inspected online - via some form of web-browser plugin; Aztex Viewer or similar. This way reviewers can see the model, and the density that the authors have built into, but not have any access to either the coordinate file or mtz - and sti make an informed judgment. With regards, from a tilting pendolino train, somewhere in the bowels of south -east England. Tony. On 19 Apr 2012, at 14:55, George M. Sheldrickgshe...@shelx.uni-ac.gwdg.de wrote: Colin, Speaking as someone who has one foot in small molecule crystallography and the other in macromolecular, I have to say that attitudes are completely different, and that there are good reasons for this. A PhD student or junior postdoc in a macromolecular lab may have spent the last three (or more) years cloning, expressing. purifying and crystallizing a protein, and it is very likely that three or more groups elsewhere in the world are working on the same target. Even if the organisms are different, usually only one group will be able to publish in a high-profile journal, so being scooped is a major worry and happens frequently, even when all concerned are completely honest. A single small molecule structure is a very much smaller part of the average chemical PhD which often involves dozens of structures, and a couple of duplicated structures will have little influence on the future career of the PhD student. Releasing the PDB hold on a structure just before submitting the paper has something to be said for it. I would like to do this more often, but it is usually vetoed by paranoid biological co-authors. Even if one is providing the competition with a good MR model, at least they will have to cite it. George On 04/19/2012 03:09 PM, Colin Groom wrote: It has always struck me as something of a surprise that pre-publication review of structures in protein-land differs so significantly from small molecule-land. One of the activities of the CCDC is to supply pre-release CSD structures to referees, using a simple, automated system to establish that the requestors are referees. This avoids the need for any involvement of the depositor or journal and allows a centralised record to be kept as to who saw which structures and when (although, to my knowledge, we have never needed to refer to this). In 2012, requests have averaged at about 5 a day, but the real figure is probably much higher, as some journals provide this facility themselves. The sense I get from the small-molecule community is that they (we) have a great degree of well placed trust and see real value in pre-publication review of structures, not just papers - I'm sure this is true for the overwhelming majority of the macromolecular world too. Colin -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of herman.schreu...@sanofi.com Sent: 19 April 2012 13:54 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers This is off course a valid point. A desperate graduate student faking a structure risks his or hers career and reputation, while an anonymous referee, borrowing someone else's results gets away without any risk of being caught. Besides making the name of the reviewer public, I see other options: 1) submit the coordinates and structure factors to the pdb to get
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Well, it is clear from this comment that in different fields there are different rules... . In macromolecular Xtallolgraphy, where some people deal with biologists from biomedical sciences, the impact of journals is an important aspect during evaluation and, unfortunately, pre-publication review of structures has no actual value in their field. For a structural BIO-logist in biomedical sciences, a paper it is not just a paper, it is an effort of years reduced to a (or few) paper(s). The non-structural BIO-people understand what is a Cell paper, but not at all about what it is a pre-publication of a structure. My thougts go in the direction of grant applications, fellowships, promotion, all filtered by the impact factor but not by pre-publication of structures which, btw, it is neither considered in the h-index of a researcher. Oh what the hell, someone else poured the gasoline, I may as well supply a lit match: What Maria says is absolutely true--I dwell among biologists, so I fully understand the rules of the field. But it's not so clear that these rules are good ones. Biology is obsessed with high impact, and I argue science is ill served by this preoccupation. The highest impact-factor journals seem to have the highest number of retractions (see this past Tuesday's New York Times Science section for a discussion). And in this forum it's certainly germane to note that the technical quality of published structures is, on average, poorer in the highest impact journals (at least by some criteria; see the paper from Brown Ramaswamy in Acta Crystallogr D63: 941-50 (2007)). Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
El 19/04/12 18:42, Patrick Loll escribió: Well, it is clear from this comment that in different fields there are different rules... . In macromolecular Xtallolgraphy, where some people deal with biologists from biomedical sciences, the impact of journals is an important aspect during evaluation and, unfortunately, pre-publication review of structures has no actual value in their field. For a structural BIO-logist in biomedical sciences, a paper it is not just a paper, it is an effort of years reduced to a (or few) paper(s). The non-structural BIO-people understand what is a Cell paper, but not at all about what it is a pre-publication of a structure. My thougts go in the direction of grant applications, fellowships, promotion, all filtered by the impact factor but not by pre-publication of structures which, btw, it is neither considered in the h-index of a researcher. Oh what the hell, someone else poured the gasoline, I may as well supply a lit match: What Maria says is absolutely true--I dwell among biologists, so I fully understand the rules of the field. But it's not so clear that these rules are good ones. Biology is obsessed with high impact, and I argue science is ill served by this preoccupation. The highest impact-factor journals seem to have the highest number of retractions (see this past Tuesday's New York Times Science section for a discussion). And in this forum it's certainly germane to note that the technical quality of published structures is, on average, poorer in the highest impact journals (at least by some criteria; see the paper from Brown Ramaswamy in Acta Crystallogr D63: 941-50 (2007)). Pat --- Patrick J. Loll, Ph. D. Professor of Biochemistry Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.l...@drexelmed.edu Indeed the rules are clearly bad. They're actually a mirror of the rules of political economy in our western/capitalist/call-them-as-you-want societies. Actually, expect bubble collapses in the biological field. Perhaps not spectacular, most probably not everything-falling-at-once, but surely not without serious implications. We also have our too-big-to-fall paradigms, especially in bio-medicine. In any case, the rules are there and for most of the people who intend to keep working (most often working as in job, not as in art) in biological science (with or without double quotes) it is certainly easier to bow to them than to resist them. Understandably, for the latter option is most often punished sooner or later, with no shame, by those who exclude you from the so-called excellence club. It would help if some big, truly respected names in biology would attack seriously these rules and put clear the damage they are causing to biological science. Some do, I'm now thinking of Peter Lawrence for example, but they are too few to be anything else than 'lone rangers'. It would be certainly even more helpful if we could unite and collectively reject this state of affairs. But this is, for several reasons that would need a far too-long text for a bulletin board post, less expected than rain on the desert. Whatever the case, we bio-crystallographers are a very small set of the people working in biology. We may now and then have this kind of discussion where we put forward our concerns, our idealistic view of the peer review system, etc. Move aside, go to a lab of almost any other field in biology and tell them about these discussions; most of the time they will look at you as they would at a Martian. Back to the original post: I have never been requested coordinates/data. It's however clear to me that if the reviewer wants to see them (s)he has the right to do so. The problem here is not with this right of the reviewer but with all the trouble caused by the current rules. If excellence, which translates in funding and salaries, had to be measured by production, what would be the problem of posting pre-prints to some central repository, as in arxiv.org, so all the people in the field could criticise/improve them? There is a time-stamp so the original authors would be acknowledged, others working the same subject could add their own findings or move to a different subject before wasting much time; designing, working and reasoning flaws might be uncovered; the role of the whole community and not just of a few big-brains would be clear for everyone to see... Keeping the rules as they are reminds me of those astronomers complicating the Ptolemaic system to save the appearances. And this is what we, you can include myself, are doing. Until the bubble collapses? -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Bosch, Juergen wrote: To pick a bit on George's point with MR citation. Here's how you can read it in the paper from your favourite competitor: A homology model was generated using [fill in any program for ab initio prediction] and subsequently used for molecular replacement with Molrep. The structure was refined to an Rwork of 21% and Rfree of 24 %. Or maybe the structure was solved by MIR, using a lot of heavy atom data that they had been unable to solve until a fortuitous MR result gave phases which located the heavy atoms -- No, No, it was that new improved version of autosol! Anyway, who cares how the heavy atoms were located- the structure was solved entirely using their data and they have the raw data (image files even) to prove it. It was just bad luck with the derivatives that kept them from solving it 6 months earlier. They really deserve to have the first publication!
[ccp4bb] Off-topic: Supplying PDB file to reviewers
Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over… Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
I always request both the final model and the experimental data (assuming that they are not yet available directly from the PDB). Obviously, this is done with assurances of confidentiality. I don't think it's common though, since I was never asked to provide the same by reviewers. What exactly is making you uncomfortable? After all, you have to release everything when your paper is accepted. Cheers, Ed. On Wed, 2012-04-18 at 22:34 +, Marc Kvansakul wrote: Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over… Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Is your structure already searchable in the PDB ? You might be able to send the validation report perhaps ? How close to publication are you ? Jürgen On Apr 18, 2012, at 6:34 PM, Marc Kvansakul wrote: Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over… Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.aumailto:m.kvansa...@latrobe.edu.au | .. Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://web.mac.com/bosch_lab/
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Marc, As someone with limited experience in publishing structures but with other experience reviewing the same I feel strongly about this. I am hoping to submit any future papers with the pdb structure already released or submit the coordinates as supplementary material. As a reviewer I find it difficult to visualise a structure based on a static 2D figure. I would like to see coordinates/structure factors supplied for review or released on the pdb. I believe that if released on the pdb then this should give you enough security that it is still your structure. Just my thoughts Joel From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Marc Kvansakul Sent: Thursday, 19 April 2012 10:34 a.m. To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Off-topic: Supplying PDB file to reviewers Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over... Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.aumailto:m.kvansa...@latrobe.edu.au |
Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers
Hi, I think this practice (requesting the data) is getting more and more common these days with some scientists having published fake structures. You are far more protected from scientific misconduct when you provide the data to referees (this takes place through an editorial system - you should keep a copy of all correspondence and requests) than you are in your own lab where your next door neighbor may decide to use your results for his/her own benefit without giving you any credit. Should your paper be rejected and if you see your structure published by others soon afterwards, you could argue with an editor that your data may have been used by others provided that you have kept a copy of everything as mentioned before in this mail. Fred. Marc Kvansakul wrote: Dear CCP4BBlers, I was wondering how common it is that reviewers request to have a copy of the PDB coordinate file for the review purpose. I have just been asked to supply this by an editor after several weeks of review, after one of the reviewers requested a copy. Not having ever been asked to do this before I feel just a tad uncomfortable about handing this over… Your opinions would be greatly appreciated. Best wishes Marc Dr. Marc Kvansakul Laboratory Head, NHMRC CDA Fellow Dept. of Biochemistry| La Trobe University | Bundoora Rm 218, Phys Sci Bld 4, Kingsbury Drive, Melbourne, 3086, Australia T: 03 9479 2263 | F: 03 9479 2467 | E: m.kvansa...@latrobe.edu.au |
